NAMIC Wiki - User contributions [en]

SidongLiu Update

2015-07-03T08:02:56Z

Sliu7418: /* Jun 09 - Jun 13 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter

* Update (2015-07-03):
** Replace the original 'Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert' to 'Slicer --launch DWIConvert'
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:
* Outline the research proposal: background, aims, methods, tasks, timelines and resources

Publication:
* Make ISBI 2014 paper submissions

 

=Dec 01 - Dec 05=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

Sonia's To do list:
*Document the steps for running Brain Visa from a neuro case
*Document the steps for running DTI Prep in Slicer4.4

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2015-07-03T08:02:29Z

Sliu7418: /* Jun 09 - Jun 13 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter

* Update (2015-07-03):
replace the original 'Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert' to 'Slicer --launch DWIConvert'
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:
* Outline the research proposal: background, aims, methods, tasks, timelines and resources

Publication:
* Make ISBI 2014 paper submissions

 

=Dec 01 - Dec 05=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

Sonia's To do list:
*Document the steps for running Brain Visa from a neuro case
*Document the steps for running DTI Prep in Slicer4.4

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T02:01:59Z

Sliu7418: /* Nov 24 - Nov 28 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:
* Outline the research proposal: background, aims, methods, tasks, timelines and resources

Publication:
* Make ISBI 2014 paper submissions

 

=Dec 01 - Dec 05=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:53:00Z

Sliu7418: /* Dec 01 - Dec 05 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:
* Prepare the outline for BCC project.

Publication:
* Make ISBI 2014 paper submissions

 

=Dec 01 - Dec 05=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:52:51Z

Sliu7418: /* Nov 24 - Nov 28 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:
* Prepare the outline for BCC project.

Publication:
* Make ISBI 2014 paper submissions

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:51:14Z

Sliu7418: /* Nov 24 - Nov 28 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

Publication:
* Make ISBI 2014 paper submissions

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:51:04Z

Sliu7418: /* Nov 10 - Nov 14 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:50:11Z

Sliu7418: /* Dec 08 - Dec 12 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

MRMD Project:
* Design the experiment for graph-based multi-modal retrieval
* Prepare the draft for Multi-modal Retrieval in Medical Domain (MRMD) Workshop at ECIR 2015.
http://www.visceral.eu/workshops/mrmd-2015/

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:45:29Z

Sliu7418: /* Nov 17 - Nov 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper, Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME.

 

=Nov 24 - Nov 28=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

Publication:
* Design the experiment for

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:44:59Z

Sliu7418: /* Nov 24 - Nov 28 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME,

 

=Nov 24 - Nov 28=

BCC Project:

* Design the website of for BCC project.
* Prepare the application for Amazon Web Service (AWS) in education research grants.
http://aws.amazon.com/education/aws-in-education-research-grants/

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

Publication:
* Design the experiment for

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:41:46Z

Sliu7418: /* Nov 17 - Nov 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Computing (BCC) project.

Publication:

* Our recent paper Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME,

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

Publication:
* Design the experiment for

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:30:28Z

Sliu7418: /* Nov 17 - Nov 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

* Literature review for Brain Connectome Project.

Publication:

* Our recent paper Multi-Modal Neuroimaging Feature Learning for Multi-Class Diagnosis of Alzheimer's Disease, is accepted to publish in IEEE TBME,

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

Publication:
* Design the experiment for

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:26:09Z

Sliu7418: /* Dec 08 - Dec 12 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

Conference:
* Prepare ICARCV 2014 slides (presented by Tom)

Publication:
* Design the experiment for

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T01:07:44Z

Sliu7418: /* Nov 17 - Nov 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

BCC Project:

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-12-10T00:31:00Z

Sliu7418: /* Nov 10 - Nov 14 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submissions
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-11-20T19:55:05Z

Sliu7418: /* Nov 03 - Nov 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
* Download and install VMTK

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submission
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-11-03T19:16:03Z

Sliu7418: /* Nov 10 - Nov 14 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
*

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition

Publication:
* Make ISBI 2014 paper submission
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-11-03T19:15:30Z

Sliu7418: /* Nov 03 - Nov 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
*

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission
* Prepare ISBI 2014 papers
 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-11-03T19:14:18Z

Sliu7418:

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
*

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-11-03T19:12:50Z

Sliu7418: /* Nov 03 - Nov 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
*

Publication:
* TBME paper review
* TBME revision submission
* ACALCI camera-ready version submission

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-11-03T19:11:08Z

Sliu7418: /* Nov 03 - Nov 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=
Lung Project:
*

Publication:
* TBME paper review

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T14:32:21Z

Sliu7418:

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD:
* Submit postdoctoral fellowship application

BWH:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD:
* Start PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T14:30:23Z

Sliu7418: /* Feb 03 - Feb 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activity:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD Activity:
* Submit postdoctoral fellowship application

BWH Activity:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH Activity:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH Activity:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH Activity:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD Activity:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD Activity:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD Activity:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD Activity:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD Activity:
* PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH Activity:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T14:29:36Z

Sliu7418: /* Nov 10 - Nov 14 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activity:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activity:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD Activity:
* Submit postdoctoral fellowship application

BWH Activity:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH Activity:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH Activity:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH Activity:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD Activity:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD Activity:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD Activity:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD Activity:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD Activity:
* PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH Activity:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Award Competition
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T14:15:31Z

Sliu7418: /* Mar 17 - Mar 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activity:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activity:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD Activity:
* Submit postdoctoral fellowship application

BWH Activity:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH Activity:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH Activity:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH Activity:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD Activity:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD Activity:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD Activity:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD Activity:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD Activity:
* PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH Activity:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T14:15:15Z

Sliu7418:

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activity:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publication:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publication:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activity:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
Publication：
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted

DTI Project:
* Reformat the Hausdorff outputs
 

=Mar 31 - Apr 4=
USYD Activity:
* Submit postdoctoral fellowship application

BWH Activity:
* Start to work at SPL, 1249 Boylston St
 

=Apr 7 - Apr 11=
Publication:
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract

DTI Project:
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 

=Apr 14 - Apr 18=
DTI Project:
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 

=Apr 21 - Apr 25=
DTI Project:
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.

USYD Activity:
* Submit the Grants-in-Aid application
 

=April 28 - May 02=
DTI Project:
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 

=May 05 - May 09=
DTI Project:
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.

Publication:
* CMIG multi-channel pattern analysis paper accepted
 

=May 12 - May 16=
DTI Project:
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.

Publication:
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 

=May 19 - May 23=
DTI Project:
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 

=May 26 - May 30=
Publication:
* Submit propagation matrix fusion paper to ICARCV 2014.

DTI Project:
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 

=Jun 02 - Jun 06=
DTI Project:
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.

NA-MIC Project:
* Invited as one of the NA-MIC tutorial contest judges.

BWH Activity:
* Attend Junichi's MRI-Robotic experiment

Publication:
* TBE Deep-Learning paper submission
 

=Jun 09 - Jun 13=
DTI Project:
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 

=Jun 16 - Jun 20=
BWH Activity:
* Prepare the DS-2019 extension

DTI Project:
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa

Publication:
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 

=Jun 23 - Jun 27=
NA-MIC Project:
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge

DTI Project:
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.

Publication:
* Prepare the DICTA 2014 abstract
 

=Jun 30 - Jul 04=
DTI Project:
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)

Publication:
* Make the submission for DICTA 2014

 
= Jul 07 - Jul 11=
BWH Activity:
* Finalize DS-2019 extension, turns out that no need to extend it

DTI Project:
* Mosaic Viewer first workable version

Publication:
* ICARCV 2014 paper accepted

USYD Activity:
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 

=Jul 14 - Jul 18=
Publication:
* Submit EMBC 2014 camera-ready version
* Submit DTIChallenge 2014 camera-ready version

USYD Activity:
* Application for Postgraduate Research Travel Scheme was approved

 
=Jul 21 - Jul 25=
Publication:
* Invited to give an oral presentation in MICCAI -MLC workshop

DTI Project:
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 

=Jul 28 - Aug 01=
USYD Activity:
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI

ADNI Project:
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 

=Aug 04 - Aug 08=
Publication:
* Submit ICARCV 2014 camera-ready version
* Make the MIA 2014 BoVW paper initial submission

USYD Activity:
* Refine Fan's visiting scholar request
 

=Aug 11 - Aug 15=
USYD Activity:
* PhD thesis writing

 
=Aug 18 - Aug 22=
DTI Project:
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 

=Aug 25 - Aug 29=
Travel:
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
BWH Activity:
* Move home to Allston

DTI Project:
* Process the dataset of 'patient4' with BrainVisa

Publication:
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
Publication:
* Prepare the MIA cross-view pattern analysis manuscript
* Submit the ACALCI 2015 abstract paper.

DTI Project:
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
DTI Project:
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=
Lung project:
* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.
 

=Oct 13 - Oct 17=
Lung Project:
* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:
* Update Slicer4 programming tutorial slides and code.
 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publication:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publication:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission
 

=Nov 03 - Nov 07=

 

=Nov 10 - Nov 14=
Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards
 

=Nov 17 - Nov 21=

 

=Nov 24 - Nov 28=

 

=Dec 01 - Dec 05=

 

=Dec 08 - Dec 12=

 

=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:59:42Z

Sliu7418: /* Feb 03 - Feb 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activity:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publications:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activities:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:59:27Z

Sliu7418: /* Mar 17 - Mar 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publications:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activities:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
Publication:
* Make EMBC 2014 paper submission

DTI Project:
* Implement a new functionality for peritumoral tract exploration
 

=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:59:03Z

Sliu7418: /* Mar 12 - Mar 14 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publications:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
BWH Activities:
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 

=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:58:50Z

Sliu7418: /* Feb 24 - Feb 28 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
Publications:
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:58:37Z

Sliu7418: /* Feb 17 - Feb 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
DTI Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:58:20Z

Sliu7418: /* Feb 17 - Feb 21 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
NA-MIC Project:
* Develop TractROIShellSeeding module in Slicer
 

=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:57:57Z

Sliu7418: /* Feb 10 - Feb 14 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
Publications:
* Prepare MICCAI 2014 papers
 

=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:57:31Z

Sliu7418: /* Feb 03 - Feb 07 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
BWH Activities:
* Attend Partners orientation - Feb 06
 

=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:55:28Z

Sliu7418: /* Jan 30 - Jan 31 */

=Jan 30 - Jan 31=
Travel:
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 

=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:55:07Z

Sliu7418: /* Oct 20 - Oct 24 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

Travel:
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
* Participate the Young Investigator Awards

 

=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:54:33Z

Sliu7418: /* Nov 10 - Nov 14 */

SidongLiu Update

2014-10-29T13:52:43Z

Sliu7418: /* Oct 27 - Oct 31 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

Publications:
* Make the TBME paper submission
* Make the MIA paper submission
* Make thesis submission

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:52:06Z

Sliu7418: /* Oct 20 - Oct 24 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
Lung Project:
* Literature review on the vessel-based lung segmentation
* Recreate the scene fro Slicer4 with the vessel models included
* Update the color code for the models

Publications:
* Finalize the MIA paper manuscript
* Finalize the TBE paper manuscript
* Finalize PhD thesis manuscript
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:50:55Z

Sliu7418: /* Oct 27 - Oct 31 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Lung Project
** Literature review on the vessel-based lung segmentation
** Recreate the scene fro Slicer4 with the vessel models included
** Update the color code for the models

* Make the MIA paper submission
* Make the TBE paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=
Lung Project:
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:50:30Z

Sliu7418: /* Oct 13 - Oct 17 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Lung Project
** Literature review on the vessel-based lung segmentation
** Recreate the scene fro Slicer4 with the vessel models included
** Update the color code for the models

* Make the MIA paper submission
* Make the TBE paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-29T13:50:05Z

Sliu7418: /* Oct 20 - Oct 24 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Lung Project
** Literature review on the vessel-based lung segmentation
** Recreate the scene fro Slicer4 with the vessel models included
** Update the color code for the models

* Make the MIA paper submission
* Make the TBE paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T20:44:03Z

Sliu7418: /* Oct 20 - Oct 24 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Literature review on the vessel-based lung segmentation
* Make the MIA paper submission
* Make the TBE paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T20:43:27Z

Sliu7418: /* Oct 20 - Oct 24 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make the MIA paper submission
* Make the TBE paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T16:32:49Z

Sliu7418: /* Oct 13 - Oct 17 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments. http://lola11.com/
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make MIA cross-view pattern analysis paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T16:08:46Z

Sliu7418: /* Oct 13 - Oct 17 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments.
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.
[Error!]
Found SharedObject Module
ModuleType: SharedObjectModule
Airway Segmentation command line:

slicer:0x127abf2c0 --processinformationaddress 0x10f4ce890 --labelValue 2 --seed 2.62861,-49.8569,-70.25 --seed 11.4569,-52.7997,-99.25 --seed -9.14251,-53.7807,-99.25 slicer:0x11370ee00#vtkMRMLScalarVolumeNode2 slicer:0x11370ee00#vtkMRMLScalarVolumeNode3

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make MIA cross-view pattern analysis paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T14:45:42Z

Sliu7418: /* Oct 13 - Oct 17 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments.
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make MIA cross-view pattern analysis paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T14:45:06Z

Sliu7418: /* Oct 27 - Oct31 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments.
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make MIA cross-view pattern analysis paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct 31=

 

=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T14:42:38Z

Sliu7418: /* Oct 20 - Oct 24 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments.
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make MIA cross-view pattern analysis paper submission
* Make PhD thesis submission
 

=Oct 27 - Oct31=

 
=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project

SidongLiu Update

2014-10-23T14:42:11Z

Sliu7418: /* Oct 06 - Oct 10 */

=Jan 30 - Jan 31=
* Depart from Sydney - Jan 30
* Arrive in Boston - Jan 31
 
=Feb 03 - Feb 07=
* Attend Partners orientation - Feb 06
 
=Feb 10 - Feb 14=
* Prepare MICCAI 2014 papers
 
=Feb 17 - Feb 21=
* Develop TractROIShellSeeding module in Slicer
 
=Feb 24 - Feb 28=
* MICCAI 2014 paper submissions
 

=Mar 12 - Mar 14=
* Attend BWH orientation
* Start to work at SPL, 75 Fransic St
 
=Mar 17 - Mar 21=
* Make EMBC 2014 paper submission
* Implement a new functionality for peritumoral tract exploration
 
=Mar 24 - Mar 28=
* Submit MICCAI 2014 paper reviews
* SNMMI 2014 abstract papers accepted
* Reformat the Hausdorff outputs
 
=Mar 31 - Apr 4=
* Submit postdoctoral fellowship application
* Start to work at SPL, 1249 Boylston St
 
=Apr 7 - Apr 11=
* Make CMIG journal paper revision submission
* Prepare the ACM MM 2014 abstract
* Work on DTI Editor module ("tract extractor")
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
* The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
* Sidong's next task would be learn qt.QImage object and see how to manipulate it in Python. Check Steve's code (https://github.com/pieper/CompareVolumes/blob/master/CompareVolumes.py)
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
=Apr 14 - Apr 18=
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
* Explore Nipype to see whether we can convert Gifti to VTK or STL, or other compatible format with Slicer (http://www.mit.edu/~satra/nipype-nightly/users/examples/dmri_connectivity.html)
* Discuss the response letter for MICCAI 2014 submissions
* Design Mosaic Viewer outlines
** Load the test data and create the scene views manually
** Link the scene views to individual 3D mosaic viewers
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
=Apr 21 - Apr 25=
* Make progress to the Mosaic Viewer module. Now it can display and manipulate multiple independent 3D viewers at the same time
* Discuss DTI Challenge preparation. Need to install Evernote and Live Minutes to enhance collaboration
* Next step would be to finalize the Mosaic Viewer by creating a scene view for the it
* Submit the Grants-in-Aid application
* The original test dataset is a HARDI dataset with 69 gradients plus 4 baselines, and we extracted 30 volumes whose b-values equal to 1000.
 
=April 28 - May 02=
* Finalize the Mosaic Viewer module.
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
** Build CLI modules (SlicerToBrainVisa Import and Export) to integrate Brain Visa morphologist tools in Slicer. Check NiftyReg extension as an example (https://github.com/spujol/niftyregExtension) and Hello World tutorial to learn how to integrate .cxx plugins (http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf). Note this tutorial might need to be updated to Slicer 4.
** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer.
** Write a simple script to 1) convert nhdr to Nifty; 2) filp left / right by changing RAS to LPI coordinate system; 3) run Morphologist pipeline in Brain Visa; 4) load output .ply file in Slicer; and 5) apply 'BrainVisatoSlicer' transform if the coordinate differences were independent to the datasets.
* Test the DWIConverter module to convert DICOM to nhdr using the datasets '...high-b.raw.gz' dataset and compare the output to '...high-b.nhdr'.
* New tasks regarding the test dataset:
** Create the tractography for extracted dataset only using single tensor algorithm
** Compare the result to that of original dataset using UKF extension
** Run the DTIPrep extension on both datasets (original and extracted)
 
=May 05 - May 09=
* Reconstruct the tensors using eigen values and eigen vectors. Slicer could not handle eigen vectors directly, so we ned to calculate the 7 coefficients in the tensor matrix.
* CMIG multi-channel pattern analysis paper accepted
 
=May 12 - May 16=
* Run DTIPrep for all the datasets.
* Clean up and classify all the processed datasets.
* Send email to Francois checking what are the differences VC and QCed results.
* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
* Run UKF tractography with 1-6 seeds per voxel, 2 tensors, other parameters by default.
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
=May 19 - May 23=
* Process the new dataset 'test1'
* Solve the DTIPrep problems.
** 1 Why there are 4 baseline images in the original dataset, but only one is left after processing?
** - All the baselines are merged into one image.
** 2. How to see the sphere after quality check?
** - We need to first save the results, and then load the XML to DTIPrep.
** 3. Why the gradient directions are changed after processing?
** - This might be a bug, resulted from rounding errors.
** 4. Why there are holes in the QCed DTI dataset?
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.
 
=May 26 - May 30=
* Submit propagation matrix fusion paper to ICARCV 2014.
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
=Jun 02 - Jun 06=
* Run BrainVisa on T1 and T2 registered data, use label map as a mask to filter out the lesion from the generated surface. Try 'Resample Scalar/Vector/DWI Volume' module, set 'Interpolation Type' to ws.
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
* Convert DICOM to FSL (nifty) format.
* Invited as one of the NA-MIC tutorial contest judges.
* Attend Junichi's MRI-Robotic experiment
* TBE Deep-Learning paper submission
 
=Jun 09 - Jun 13=
* Test DWIConvert on Sample Data - DWIVolume
** NrrdToFSL: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode NrrdToFSL --inputVolume ./dwi.nhdr --outputVolume ./dwi_fsl.nii.gz --outputBValues ./bvals.txt --outputBVectors ./bvec.txt
** FSLToNrrd: Slicer-build/lib/Slicer-4.3/cli-modules/DWIConvert --conversionMode FSLToNrrd --inputVolume ./dwi_fsl.nii.gz --outputVolume ./dwi_reconverted.nrrd --inputBValues ./bvals.txt --inputBVectors ./bvec.txt
* Process the dataset of 'test1' with DWIConverter
 
=Jun 16 - Jun 20=
* Prepare the DS-2019 extension
* Process the dataset of 'patient2' with BrainVisa
* Process the dataset of 'patient3' with BrainVisa
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.
 
=Jun 23 - Jun 27=
* NA-MIC 2014 SUMMER PROJECT WEEK
* CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
* Serve as NA-MIC tutorial contest judge
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
* Prepare the DICTA 2014 abstract
 
=Jun 30 - Jul 04=
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
* Test 'DICOM-TO-NIFTI-CONVERTER' matlab toolbox (http://www.mathworks.com/matlabcentral/fileexchange/41874-dicom-to-nifti-converter/content/dicom2nifti.m). However, this toolbox is not usable for our SIEMENS data, because it only work with DICOM files from Phillips Achieva 3T R2.6 with
** Slice orientation : transverse
** Patient position : head first
** Patient orientation: supine
** Fold-over direction: AP
** Fat shift direction: P
** Gradient resolution: high (DTI)
** Gradient overplus : yes (DTI)
** Sort images : b=0 volume first (DTI)
* Make the submission for DICTA 2014
 
= Jul 07 - Jul 11=
* Finalize DS-2019 extension, turns out that no need to extend it
* Mosaic Viewer first workable version
* ICARCV 2014 paper accepted
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
=Jul 14 - Jul 18=
* Submit EMBC 2014 camera-ready version
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
 
=Jul 21 - Jul 25=
* Invited to give an oral presentation in MICCAI -MLC workshop
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
=Jul 28 - Aug 01=
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
=Aug 04 - Aug 08=
* Submit ICARCV 2014 camera-ready version
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
=Aug 11 - Aug 15=
* PhD thesis writing
 
=Aug 18 - Aug 22=
* Add a new feature in Mosaic Viewer. Now all the viewers can be synchronized through the 'Sync Camera' function.
** Step 1: load or create the scene views
** Step 2: select the master viewer where the user defines the orientation via 'view to synchronize' drop list.
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.
 
=Aug 25 - Aug 29=
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.
 

=Sep 01 - Sep 05=
* Move home to Allston
* Process the dataset of 'patient4' with BrainVisa
* Prepare the ACALCI 2015 abstract
 

=Sep 08 - Sep 12=
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
* Submit the ACALCI 2015 abstract paper.
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
* DTI Challenge logistics
** Attend the DTIChallenge preparation meeting, arrange the conference room and test the systems.
** Process the dataset for patient 3 with BrainVisa.
** Summarize the DTI Challenge review results.
** Generate the box plots for DTI Challenge review results.
** Prepare the envelops and folders.
** Print out the onsite review forms.
** Prepare the USB keys.
 

=Sep 14 - Sep 19=
* Attend the MICCAI DTI Challenge, Sep 14
* Attend the MICCAI main conference, Sep 15 - Sep 17
* Attend the MICCAI CADDementia Challenge, Sep 18 morning
* Attend the MICCAI Machine Learning Challenge, Sep 18 afternoon
 

=Sep 22 - Oct 03=
* Two weeks' leave
 

=Oct 06 - Oct 10=

Lung project:

* Manually draw the boundaries between the bronchi in right lung
* Generate the models using the Draw Model tool in Slicer 3.6.4.
* Save the models and the scene and check their compatibility with Slicer 4.

 

=Oct 13 - Oct 17=

Lung Project:

* Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
* Regenerate the models for the dataset
* Literature review on automated segmentation of lung segments.
* Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
* Try airway segmentation on Slicer 4 with lung project dataset.

NA-MIC Project:

* Update Slicer4 programming tutorial slides and code.

 

=Oct 20 - Oct 24=
* Make MIA submission
* Make PhD thesis submission
 

=Oct 27 - Oct31=

 
=Nov 03 - Nov 07=

 
=Nov 10 - Nov 14=

 
=Nov 17 - Nov 21=

 
=Nov 24 - Nov 28=

 
=Dec 01 - Dec 05=

 
=Dec 08 - Dec 12=

 
=Dec 15 - Dec 19=
* End of project