Difference between revisions of "SidongLiu Update"

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** 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.
 +
 +
* May 12 - May 16
 
** 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.
Line 66: Line 68:
 
** 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.
  
* May 12 - May 16
+
* May 19 - May 23
 
** Process the new dataset 'test1'
 
** Process the new dataset 'test1'
 
** Solve the DTIPrep problems.
 
** Solve the DTIPrep problems.
Line 72: Line 74:
 
*** 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.  
*** 4. Why there are holes in the QCed DTI dataset? We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'. After testing with different settings, we found when this parameter is set to less than 50, the holes disappear.
+
*** 4. Why there are holes in the QCed DTI dataset? We need to reset the parameter 'DTI_bCompute - DTI_baselineThreshold'.  
  
* May 19 - May 23
+
* 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.
 +
 +
* Jun 2 - Jun 6
 
** 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.
 
+
** Invited to be NA-MIC tutorial contest judge.
* May 26 - May 30
+
** Attend Junichi's experiment
* Jun 2 - Jun 6
 

Revision as of 14:58, 5 June 2014

Home < SidongLiu Update
  • Feb 28
    • MICCAI paper submissions
  • Mar 12 - 14
    • Start to work at SPL, 75 Fransic St
  • Mar 17 - 21
    • EMBC paper submission
    • Implement a new functionality for peritumoral tract exploration
  • Mar 24 - 28
    • MICCAI paper reviews
    • SNMMI abstract papers accepted
    • Reformat the Hausdorff outputs
  • Mar 31 - Apr 4
    • Postdoctoral fellowship application
    • Start to work at SPL, Boylston St
  • April 7-11
    • CMIG journal revised version submission
    • ACM MM abstract preparation
    • Work on DTI Editor module ("tract extractor")
  • April 21-25
    • 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 2 - Jun 6
    • 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