Difference between revisions of "SidongLiu Update"
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** 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 | ** 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 | * 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' | ||
<br \> | <br \> | ||
− | |||
=Jun 16 - Jun 20= | =Jun 16 - Jun 20= | ||
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* Participate the Young Investigator Award Competition | * Participate the Young Investigator Award Competition | ||
− | |||
− | |||
<br \> | <br \> | ||
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BCC Project: | BCC Project: | ||
+ | * Outline the research proposal: background, aims, methods, tasks, timelines and resources | ||
− | + | Publication: | |
− | * | + | * Make ISBI 2014 paper submissions |
− | |||
+ | <br \> | ||
+ | =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/ | ||
<br \> | <br \> | ||
− | |||
=Dec 08 - Dec 12= | =Dec 08 - Dec 12= | ||
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* Prepare ICARCV 2014 slides (presented by Tom) | * Prepare ICARCV 2014 slides (presented by Tom) | ||
− | + | MRMD Project: | |
− | * Design the experiment for | + | * 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 | ||
<br \> | <br \> |
Latest revision as of 08:02, 3 July 2015
Home < SidongLiu UpdateContents
- 1 Jan 30 - Jan 31
- 2 Feb 03 - Feb 07
- 3 Feb 10 - Feb 14
- 4 Feb 17 - Feb 21
- 5 Feb 24 - Feb 28
- 6 Mar 12 - Mar 14
- 7 Mar 17 - Mar 21
- 8 Mar 24 - Mar 28
- 9 Mar 31 - Apr 4
- 10 Apr 7 - Apr 11
- 11 Apr 14 - Apr 18
- 12 Apr 21 - Apr 25
- 13 April 28 - May 02
- 14 May 05 - May 09
- 15 May 12 - May 16
- 16 May 19 - May 23
- 17 May 26 - May 30
- 18 Jun 02 - Jun 06
- 19 Jun 09 - Jun 13
- 20 Jun 16 - Jun 20
- 21 Jun 23 - Jun 27
- 22 Jun 30 - Jul 04
- 23 Jul 07 - Jul 11
- 24 Jul 14 - Jul 18
- 25 Jul 21 - Jul 25
- 26 Jul 28 - Aug 01
- 27 Aug 04 - Aug 08
- 28 Aug 11 - Aug 15
- 29 Aug 18 - Aug 22
- 30 Aug 25 - Aug 29
- 31 Sep 01 - Sep 05
- 32 Sep 08 - Sep 12
- 33 Sep 14 - Sep 19
- 34 Sep 22 - Oct 03
- 35 Oct 06 - Oct 10
- 36 Oct 13 - Oct 17
- 37 Oct 20 - Oct 24
- 38 Oct 27 - Oct 31
- 39 Nov 03 - Nov 07
- 40 Nov 10 - Nov 14
- 41 Nov 17 - Nov 21
- 42 Nov 24 - Nov 28
- 43 Dec 01 - Dec 05
- 44 Dec 08 - Dec 12
- 45 Dec 15 - Dec 19
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 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