Difference between revisions of "SidongLiu Update"
From NAMIC Wiki
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* Feb 24 - Feb 28 | * Feb 24 - Feb 28 | ||
− | ** Partners orientation | + | ** Attend the Partners orientation |
** MICCAI 2014 paper submissions | ** MICCAI 2014 paper submissions | ||
<br \> | <br \> | ||
* Mar 12 - Mar 14 | * Mar 12 - Mar 14 | ||
− | ** 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 | ||
− | ** EMBC 2014 paper submission | + | ** Make EMBC 2014 paper submission |
** 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 | ||
− | ** MICCAI 2014 paper reviews | + | ** Submit MICCAI 2014 paper reviews |
** SNMMI 2014 abstract papers accepted | ** SNMMI 2014 abstract papers accepted | ||
** Reformat the Hausdorff outputs | ** Reformat the Hausdorff outputs | ||
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** 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) | ||
** Discuss the response letter for MICCAI 2014 submissions | ** Discuss the response letter for MICCAI 2014 submissions | ||
− | ** | + | ** Design Mosaic Viewer outlines |
*** Load the test data and create the scene views manually | *** Load the test data and create the scene views manually | ||
*** Link the scene views to individual 3D mosaic viewers | *** Link the scene views to individual 3D mosaic viewers | ||
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<br \> | <br \> | ||
* Apr 21 - Apr 25 | * 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 | ** 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. | ** 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 | ||
− | ** | + | ** Finalize the Mosaic Viewer module. |
− | ** Successfully | + | ** 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 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. | *** Build a Python wrapper which point to the Brain Visa executable files and run Brain Visa in Slicer. | ||
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* May 05 - May 09 | * 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. | ** 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 |
<br \> | <br \> | ||
* May 12 - May 16 | * May 12 - May 16 | ||
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** Process the new dataset 'test1' | ** Process the new dataset 'test1' | ||
** Solve the DTIPrep problems. | ** Solve the DTIPrep problems. | ||
− | *** | + | *** # 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. | *** 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. | *** 3. Why the gradient directions are changed after processing? This might be a bug, resulted from rounding errors. |
Revision as of 14:52, 9 July 2014
Home < SidongLiu Update- Feb 24 - Feb 28
- Attend the Partners orientation
- 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.
- May 19 - May 23
- Process the new dataset 'test1'
- Solve the DTIPrep problems.
- # 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 to be NA-MIC tutorial contest judge.
- Attend Junichi's experiment
- 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
- Test DWIConvert on 'test1' dataset
- Test DWIConvert on Sample Data - DWIVolume
- 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 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
- Prepare the DICTA 2014 abstract
- Jun 30 - Jul 04
- Reprocess the dataset of patient2_1 with DWI Converter
- 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 paper accepted
- Be awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship.