Difference between revisions of "SidongLiu Update"

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=Jan 30 - Jan 31=
 
=Jan 30 - Jan 31=
 +
Travel:
 
* Depart from Sydney - Jan 30
 
* Depart from Sydney - Jan 30
 
* Arrive in Boston - Jan 31
 
* Arrive in Boston - Jan 31
 
<br \>
 
<br \>
 +
 +
 
=Feb 03 - Feb 07=
 
=Feb 03 - Feb 07=
 +
BWH:
 
* Attend Partners orientation - Feb 06
 
* Attend Partners orientation - Feb 06
 
<br \>
 
<br \>
 +
 
=Feb 10 - Feb 14=
 
=Feb 10 - Feb 14=
 +
Publication:
 
* Prepare MICCAI 2014 papers
 
* Prepare MICCAI 2014 papers
 
<br \>
 
<br \>
 +
 +
 
=Feb 17 - Feb 21=
 
=Feb 17 - Feb 21=
 +
DTI Project:
 
* Develop TractROIShellSeeding module in Slicer
 
* Develop TractROIShellSeeding module in Slicer
 
<br \>
 
<br \>
 +
 +
 
=Feb 24 - Feb 28=
 
=Feb 24 - Feb 28=
 +
Publication:
 
* MICCAI 2014 paper submissions
 
* MICCAI 2014 paper submissions
 
<br \>
 
<br \>
 +
  
 
=Mar 12 - Mar 14=
 
=Mar 12 - Mar 14=
 +
BWH:
 
* Attend BWH orientation
 
* Attend BWH orientation
 
* Start to work at SPL, 75 Fransic St
 
* Start to work at SPL, 75 Fransic St
 
<br \>
 
<br \>
 +
 +
 
=Mar 17 - Mar 21=
 
=Mar 17 - Mar 21=
 +
Publication:
 
* Make EMBC 2014 paper submission
 
* Make EMBC 2014 paper submission
 +
 +
DTI Project:
 
* Implement a new functionality for peritumoral tract exploration
 
* Implement a new functionality for peritumoral tract exploration
 
<br \>
 
<br \>
 +
 
=Mar 24 - Mar 28=
 
=Mar 24 - Mar 28=
 +
Publication:
 
* Submit MICCAI 2014 paper reviews
 
* Submit MICCAI 2014 paper reviews
 
* SNMMI 2014 abstract papers accepted
 
* SNMMI 2014 abstract papers accepted
 +
 +
DTI Project:
 
* Reformat the Hausdorff outputs
 
* Reformat the Hausdorff outputs
 
<br \>
 
<br \>
 +
 
=Mar 31 - Apr 4=
 
=Mar 31 - Apr 4=
 +
USYD:
 
* Submit postdoctoral fellowship application
 
* Submit postdoctoral fellowship application
 +
 +
BWH:
 
* Start to work at SPL, 1249 Boylston St
 
* Start to work at SPL, 1249 Boylston St
 
<br \>
 
<br \>
 +
 +
 
=Apr 7 - Apr 11=
 
=Apr 7 - Apr 11=
 +
Publication:
 
* Make CMIG journal paper revision submission  
 
* Make CMIG journal paper revision submission  
 
* Prepare the ACM MM 2014 abstract
 
* Prepare the ACM MM 2014 abstract
 +
 +
DTI Project:
 
* Work on DTI Editor module ("tract extractor")
 
* Work on DTI Editor module ("tract extractor")
 
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
 
* The fiber selection function can be found in Diffusion -> Tractography -> FiberBundleLabelSelect module.
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* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
* A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
<br \>
 
<br \>
 +
 +
 
=Apr 14 - Apr 18=
 
=Apr 14 - Apr 18=
 +
DTI Project:
 
* Try Brain Visa trick on mac (http://brainvisa.info/forum/viewtopic.php?f=2&t=1713#p6399)
 
* 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)
 
* 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)
Line 51: Line 86:
 
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
<br \>
 
<br \>
 +
 +
 
=Apr 21 - Apr 25=
 
=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
 
* 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
 
* 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
 
* 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
 
* 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.
 
 
<br \>
 
<br \>
 +
 +
 
=April 28 - May 02=
 
=April 28 - May 02=
 +
DTI Project:
 
* Finalize the Mosaic Viewer module.  
 
* 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:
 
* Successfully load and corrected the Brain Visa surface files into Slicer. Next step would be streamline the process. There might be three potential solutions:
Line 70: Line 113:
 
** Run the DTIPrep extension on both datasets (original and extracted)
 
** Run the DTIPrep extension on both datasets (original and extracted)
 
<br \>
 
<br \>
 +
 +
 
=May 05 - May 09=
 
=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.  
 
* 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
 
* CMIG multi-channel pattern analysis paper accepted
 
<br \>
 
<br \>
 +
 +
 
=May 12 - May 16=
 
=May 12 - May 16=
 +
DTI Project:
 
* Run DTIPrep for all the datasets.  
 
* Run DTIPrep for all the datasets.  
 
* Clean up and classify all the processed datasets.
 
* Clean up and classify all the processed datasets.
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* Send BrainVisa screenshots to Sonia, describing the sulci recognition problems.
 
* 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.
 
* 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
 
* CMIG multi-channel pattern analysis paper available online http://www.sciencedirect.com/science/article/pii/S0895611114000639
 
<br \>
 
<br \>
 +
 +
 
=May 19 - May 23=
 
=May 19 - May 23=
 +
DTI Project:
 
* Process the new dataset 'test1'
 
* Process the new dataset 'test1'
 
* Solve the DTIPrep problems.
 
* Solve the DTIPrep problems.
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** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.  
 
** - We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.  
 
<br \>
 
<br \>
 +
 +
 
=May 26 - May 30=
 
=May 26 - May 30=
 +
Publication:
 
* Submit propagation matrix fusion paper to ICARCV 2014.
 
* 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.
 
* Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
<br \>
 
<br \>
 +
 +
 
=Jun 02 - Jun 06=
 
=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 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.
 
* Run 'Slicer Surface Toolbox' to refine BrainVisa surface. Chcek 'splitting' box in Normals.
 
* Convert DICOM to FSL (nifty) format.
 
* Convert DICOM to FSL (nifty) format.
 +
 +
NA-MIC Project:
 
* Invited as one of the NA-MIC tutorial contest judges.
 
* Invited as one of the NA-MIC tutorial contest judges.
 +
 +
BWH:
 
* Attend Junichi's MRI-Robotic experiment
 
* Attend Junichi's MRI-Robotic experiment
 +
 +
Publication:
 
* TBE Deep-Learning paper submission
 
* TBE Deep-Learning paper submission
 
<br \>
 
<br \>
 +
 +
 
=Jun 09 - Jun 13=
 
=Jun 09 - Jun 13=
 +
DTI Project:
 
* Test DWIConvert on Sample Data - DWIVolume
 
* 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
 
** 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
 
** 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=
 +
BWH:
 
* Prepare the DS-2019 extension
 
* Prepare the DS-2019 extension
 +
 +
DTI Project:
 
* Process the dataset of 'patient2' with BrainVisa
 
* Process the dataset of 'patient2' with BrainVisa
 
* Process the dataset of 'patient3' 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.  
 
* MICCAI 2014 Machine Learning Challenge (MLC) result was revealed and we ranked 10th in 50 teams.  
 
<br \>
 
<br \>
 +
 +
 
=Jun 23 - Jun 27=
 
=Jun 23 - Jun 27=
 +
NA-MIC Project:
 
* NA-MIC 2014 SUMMER PROJECT WEEK
 
* 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)
 
* 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
 
* Serve as NA-MIC tutorial contest judge
 +
 +
DTI Project:
 
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
 
* Process the dataset of 'patient2_1' with DWIConverter. The b-values were found wrong.
 +
 +
Publication:
 
* Prepare the DICTA 2014 abstract
 
* Prepare the DICTA 2014 abstract
 
<br \>
 
<br \>
 +
 +
 
=Jun 30 - Jul 04=
 
=Jun 30 - Jul 04=
 +
DTI Project:
 
* Reprocess the dataset of 'patient2_1' with DWI Converter. The b-values seem correct.
 
* 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  
 
* 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  
Line 136: Line 228:
 
** Gradient overplus  : yes (DTI)
 
** Gradient overplus  : yes (DTI)
 
** Sort images        : b=0 volume first (DTI)
 
** Sort images        : b=0 volume first (DTI)
 +
 +
Publication:
 
* Make the submission for DICTA 2014
 
* Make the submission for DICTA 2014
 +
 +
 
<br \>
 
<br \>
 
= Jul 07 - Jul 11=
 
= Jul 07 - Jul 11=
 +
BWH:
 
* Finalize DS-2019 extension, turns out that no need to extend it
 
* Finalize DS-2019 extension, turns out that no need to extend it
 +
 +
DTI Project:
 
* Mosaic Viewer first workable version
 
* Mosaic Viewer first workable version
 +
 +
Publication:
 
* ICARCV 2014 paper accepted
 
* ICARCV 2014 paper accepted
 +
 +
USYD:
 
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
* Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship
 
<br \>
 
<br \>
 +
 +
 
=Jul 14 - Jul 18=
 
=Jul 14 - Jul 18=
 +
Publication:
 
* Submit EMBC 2014 camera-ready version
 
* Submit EMBC 2014 camera-ready version
 +
* Submit DTIChallenge 2014 camera-ready version
 +
 +
USYD:
 
* Application for Postgraduate Research Travel Scheme was approved
 
* Application for Postgraduate Research Travel Scheme was approved
* Submit DTIChallenge 2014 camera-ready version
+
 
 +
 
 
<br \>
 
<br \>
 
=Jul 21 - Jul 25=
 
=Jul 21 - Jul 25=
 +
Publication:
 
* Invited to give an oral presentation in MICCAI -MLC workshop
 
* 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.
 
* Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.
 
<br \>
 
<br \>
 +
 +
 
=Jul 28 - Aug 01=
 
=Jul 28 - Aug 01=
 +
USYD:
 
* Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
 
* 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%.
 
* Test new FreeSurfer features extracted from the ADNI datasets by UCSF lab, the performance of multi-class classification (NC/MCI/AD) is 81.25%.
 
<br \>
 
<br \>
 +
 +
 
=Aug 04 - Aug 08=
 
=Aug 04 - Aug 08=
 +
Publication:
 
* Submit ICARCV 2014 camera-ready version
 
* Submit ICARCV 2014 camera-ready version
 +
* Make the MIA 2014 BoVW paper initial submission
 +
 +
USYD:
 
* Refine Fan's visiting scholar request
 
* Refine Fan's visiting scholar request
* Make the MIA 2014 BoVW paper initial submission
 
 
<br \>
 
<br \>
 +
 +
 
=Aug 11 - Aug 15=
 
=Aug 11 - Aug 15=
* PhD thesis writing
+
USYD:
 +
* Start PhD thesis writing
 +
 
 +
 
 
<br \>
 
<br \>
 
=Aug 18 - Aug 22=
 
=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.  
 
* 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 1: load or create the scene views
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** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.  
 
** Step 3: click 'Sync Camera' button, the orientation will propagate to all other viewers.  
 
<br \>
 
<br \>
 +
 +
 
=Aug 25 - Aug 29=
 
=Aug 25 - Aug 29=
 +
Travel:
 
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.  
 
* Attend EMBC 2014 conference in Chicago, Sep 27 - 31.  
 
<br \>
 
<br \>
  
 
=Sep 01 - Sep 05=
 
=Sep 01 - Sep 05=
 +
BWH:
 
* Move home to Allston
 
* Move home to Allston
 +
 +
DTI Project:
 
* Process the dataset of 'patient4' with BrainVisa
 
* Process the dataset of 'patient4' with BrainVisa
 +
 +
Publication:
 
* Prepare the ACALCI 2015 abstract
 
* Prepare the ACALCI 2015 abstract
 
<br \>
 
<br \>
 +
  
 
=Sep 08 - Sep 12=
 
=Sep 08 - Sep 12=
 +
Publication:
 
* Prepare the MIA cross-view pattern analysis manuscript
 
* Prepare the MIA cross-view pattern analysis manuscript
* Finalize PhD thesis
 
 
* Submit the ACALCI 2015 abstract paper.
 
* 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.
 
* Process the datasets for patient 4 with DTIPrep, including the original DWI dataset and the truncated DWI dataset.
 
* DTI Challenge logistics
 
* DTI Challenge logistics
Line 196: Line 336:
 
<br \>
 
<br \>
  
=Sep 15 - Sep 19=
+
 
* Attend MICCAI 2014 conference in Boston
+
=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
 
<br \>
 
<br \>
 +
 +
 
=Sep 22 - Oct 03=
 
=Sep 22 - Oct 03=
 
* Two weeks' leave
 
* Two weeks' leave
Line 204: Line 351:
  
 
=Oct 06 - Oct 10=
 
=Oct 06 - Oct 10=
 
 
Lung project:  
 
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.
 +
<br \>
  
Graw 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.
 
  
<br \>
+
=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:
  
=Oct 13 - Oct 17=
+
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
  
Todo List:
 
  
Update tutorial slides
+
NA-MIC Project:
 +
* Update Slicer4 programming tutorial slides and code.
 +
<br \>
  
Update color look up table
 
  
Try airway segmentation on Slicer 4 with lung project dataset.
+
=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
  
Check the connectivity tool with Jessica.
+
Publication:
 +
* Finalize the MIA paper manuscript
 +
* Finalize the TBE paper manuscript
 +
* Finalize PhD thesis manuscript
 +
<br \ >
  
 +
=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
 
<br \>
 
<br \>
  
=Oct 20 - Oct 24=
 
  
<br \ >
+
=Nov 03 - Nov 07=
=Oct 27 - Oct31=
+
Lung Project:
 +
* Download and install VMTK
  
 +
Publication:
 +
* TBME paper review
 +
* TBME revision submission
 +
* ACALCI camera-ready version submission
 +
* Prepare ISBI 2014 papers
 
<br \>
 
<br \>
=Nov 03 - Nov 07=
 
  
<br \>
 
 
=Nov 10 - Nov 14=
 
=Nov 10 - Nov 14=
 +
Travel:
 +
* Attend the [http://gcbme.embs.org/brain2014/ IEEE EMBS Grand Challenge Conference]
 +
* Participate the Young Investigator Award Competition
  
 
<br \>
 
<br \>
 +
 
=Nov 17 - Nov 21=
 
=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.
  
 
<br \>
 
<br \>
 +
 
=Nov 24 - Nov 28=
 
=Nov 24 - Nov 28=
 +
 +
BCC Project:
 +
* Outline the research proposal: background, aims, methods, tasks, timelines and resources
 +
 +
Publication:
 +
* Make ISBI 2014 paper submissions
  
 
<br \>
 
<br \>
 +
 
=Dec 01 - Dec 05=
 
=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=
 +
 +
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
  
 
<br \>
 
<br \>
 +
 
=Dec 15 - Dec 19=
 
=Dec 15 - Dec 19=
 
* End of project
 
* End of project
 
<br \>
 
<br \>

Latest revision as of 08:02, 3 July 2015

Home < SidongLiu Update

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:



Apr 14 - Apr 18

DTI Project:



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:



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:

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:

[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:

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:


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