Difference between revisions of "SidongLiu Update"

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* Mar 12 - Mar 14
 
* Mar 12 - Mar 14
 
** Start to work at SPL, 75 Fransic St
 
** Start to work at SPL, 75 Fransic St
 
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* Mar 17 - Mar 21
 
* Mar 17 - Mar 21
 
** EMBC 2014 paper submission
 
** EMBC 2014 paper submission
 
** Implement a new functionality for peritumoral tract exploration
 
** Implement a new functionality for peritumoral tract exploration
 
+
<br \>
 
* Mar 24 - Mar 28
 
* Mar 24 - Mar 28
 
** MICCAI 2014 paper reviews
 
** 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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<br \>
 
* Mar 31 - Apr 4
 
* Mar 31 - Apr 4
 
** Submit postdoctoral fellowship application
 
** Submit postdoctoral fellowship application
 
** Start to work at SPL, Boylston St
 
** Start to work at SPL, Boylston St
 
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* Apr 7 - Apr 11
 
* Apr 7 - Apr 11
 
** Make CMIG journal paper revision submission  
 
** Make CMIG journal paper revision submission  
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** 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)
 
** 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.
 
** A control panel style mosaic to flexibly display different teams or patients. A summary table showing the statistics.
 
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* Apr 14 - Apr 18
 
* Apr 14 - Apr 18
 
** 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)
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*** Link the scene views to individual 3D mosaic viewers
 
*** 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
 
*** Test one MRI volume in 4 viewers first; then test 4 MRI volumes in 4 viewers; finally test the DTI data
 
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<br \>
 
* Apr 21 - Apr 25
 
* Apr 21 - Apr 25
 
** Made progress to the Mosaic Viewer module. Now it could display and manipulate multiple independent 3D viewers at the same time
 
** Made progress to the Mosaic Viewer module. Now it could display and manipulate multiple independent 3D viewers at the same time
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** Submitted the Grants-in-Aid application
 
** Submitted 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 \>
 
* April 28 - May 02
 
* April 28 - May 02
 
** Finalized the Mosaic Viewer module.  
 
** Finalized the Mosaic Viewer module.  
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*** Compare the result to that of original dataset using UKF extension
 
*** Compare the result to that of original dataset using UKF extension
 
*** Run the DTIPrep extension on both datasets (original and extracted)
 
*** Run the DTIPrep extension on both datasets (original and extracted)
 
+
<br \>
 
* 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.  
 
** Our multi-channel pattern analysis paper was accepted by CMIG.
 
** Our multi-channel pattern analysis paper was accepted by CMIG.
 
+
<br \>
 
* May 12 - May 16
 
* May 12 - May 16
 
** Run DTIPrep for all the datasets.  
 
** Run DTIPrep for all the 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.
 
+
<br \>
 
* May 19 - May 23
 
* May 19 - May 23
 
** Process the new dataset 'test1'
 
** Process the new dataset 'test1'
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*** 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.  
 
*** 4. Why there are holes in the QCed DTI dataset? We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.  
 
*** 4. Why there are holes in the QCed DTI dataset? We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.  
 
+
<br \>
 
* May 26 - May 30
 
* May 26 - May 30
 
** Submit propagation matrix fusion paper to ICARCV 2014.
 
** 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.
 
** Rerun DTIPrep on 'test1'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
 
+
<br \>
 
* Jun 02 - Jun 06
 
* 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 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.
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** Invited to be NA-MIC tutorial contest judge.
 
** Invited to be NA-MIC tutorial contest judge.
 
** Attend Junichi's experiment
 
** Attend Junichi's experiment
 
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<br \>
 
* Jun 09 - Jun 13
 
* Jun 09 - Jun 13
 
** Test DWIConvert on Sample Data - DWIVolume
 
** Test DWIConvert on Sample Data - DWIVolume
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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
 
** Test DWIConvert on 'test1' dataset
 
** Test DWIConvert on 'test1' dataset
 
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<br \>
 
* Jun 16 - Jun 20
 
* Jun 16 - Jun 20
 
** Prepare the DS-2019 extension
 
** Prepare the DS-2019 extension
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** Process the dataset of patient3 with BrainVisa
 
** Process the dataset of patient3 with BrainVisa
 
** MICCAI 2014 Machine Learning Challenge result was revealed and we ranked 10th in 50 teams.  
 
** MICCAI 2014 Machine Learning Challenge result was revealed and we ranked 10th in 50 teams.  
 
+
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* Jun 23 - Jun 27 (NA-MIC 2014 SUMMER PROJECT WEEK)
 
* 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)
 
** CAD Toolbox for Neurodegenerative Disease Diagnosis (http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week:CAD_Toolbox_for_Neurological_Disorders)
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** Process the dataset of patient2_1 with DWIConverter
 
** Process the dataset of patient2_1 with DWIConverter
 
** Prepare the DICTA 2014 abstract
 
** Prepare the DICTA 2014 abstract
 
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<br \>
 
* Jun 30 - Jul 04
 
* Jun 30 - Jul 04
 
** Reprocess the dataset of patient2_1 with DWI Converter
 
** Reprocess the dataset of patient2_1 with DWI Converter
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*** Sort images        : b=0 volume first (DTI)
 
*** Sort images        : b=0 volume first (DTI)
 
** Make the submission for DICTA 2014
 
** Make the submission for DICTA 2014
 
+
<br \>
 
*  Jul 07 - Jul 11
 
*  Jul 07 - Jul 11
 
** Finalize DS-2019 extension, turns out that no need to extend it
 
** Finalize DS-2019 extension, turns out that no need to extend it
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** ICARCV paper accepted
 
** ICARCV paper accepted
 
** Be awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship.
 
** Be awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship.
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Revision as of 14:43, 9 July 2014

Home < SidongLiu Update
  • Feb 24 - Feb 28
    • MICCAI 2014 paper submissions


  • Mar 12 - Mar 14
    • Start to work at SPL, 75 Fransic St


  • Mar 17 - Mar 21
    • EMBC 2014 paper submission
    • Implement a new functionality for peritumoral tract exploration


  • Mar 24 - Mar 28
    • 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, Boylston St




  • Apr 21 - Apr 25
    • Made progress to the Mosaic Viewer module. Now it could display and manipulate multiple independent 3D viewers at the same time
    • Discussed 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
    • Submitted 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
    • Finalized the Mosaic Viewer module.
    • Successfully loaded 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.
    • Our multi-channel pattern analysis paper was accepted by CMIG.


  • 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.
      • 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 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


  • 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 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.