Difference between revisions of "SidongLiu Update"

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* Arrive in Boston - Jan 31
 
* Arrive in Boston - Jan 31
 
<br \>
 
<br \>
= Feb 03 - Feb 07=
+
=Feb 03 - Feb 07=
 
* Attend Partners orientation - Feb 06
 
* Attend Partners orientation - Feb 06
 
<br \>
 
<br \>
Line 16: Line 16:
 
* MICCAI 2014 paper submissions
 
* MICCAI 2014 paper submissions
 
<br \>
 
<br \>
* Mar 12 - Mar 14
+
=Mar 12 - Mar 14=
** 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=
** Make 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=
** Submit 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
 
<br \>
 
<br \>
* Mar 31 - Apr 4
+
=Mar 31 - Apr 4=
** Submit postdoctoral fellowship application
+
* Submit postdoctoral fellowship application
** 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=
** Make CMIG journal paper revision submission  
+
* Make CMIG journal paper revision submission  
** Prepare the ACM MM 2014 abstract
+
* Prepare the ACM MM 2014 abstract
** 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.
** The fiber bundle cropping function can be found in Tractography Display module (http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/TractographyDisplay)
+
* 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)
+
* 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.
 
<br \>
 
<br \>
* 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)
** 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
+
* 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
*** 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=
** 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
** 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.
+
* 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.  
 
** 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:

Revision as of 19:33, 6 August 2014

Home < SidongLiu Update

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

  • 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


Apr 14 - Apr 18


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.
    • Be 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 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 paper accepted
    • Be awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship.