SidongLiu Update

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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

  • 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.
  • 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 23 - Jun 27


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 2014 paper accepted
  • Awarded the Sydney University Graduates Union of North America (SUGUNA) Alumni Scholarship


Jul 14 - Jul 18

  • Submit EMBC 2014 camera-ready version
  • Application for Postgraduate Research Travel Scheme was approved
  • Submit DTIChallenge 2014 camera-ready version


Jul 21 - Jul 25

  • Invited to give an oral presentation in MICCAI -MLC workshop
  • Update Mosaic Viewer. Now it can restore the exact snapshot as saved in the scene views.


Jul 28 - Aug 01

  • Co-supervise Tom's new student, Nur, on his 18pt research project - Feature Extraction and Coding for Diffusion MRI
  • 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

  • Submit ICARCV 2014 camera-ready version
  • Refine Fan's visiting scholar request
  • Make the MIA 2014 BoVW paper initial submission


Aug 11 - Aug 15

  • PhD thesis writing


Aug 18 - Aug 22

  • 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

  • Attend EMBC 2014 conference in Chicago, Sep 27 - 31.


Sep 01 - Sep 05

  • Move home to Allston
  • Process the dataset of 'patient4' with BrainVisa
  • Prepare the ACALCI 2015 abstract


Sep 08 - Sep 12

  • Prepare the MIA cross-view pattern analysis manuscript
  • Finalize PhD thesis
  • Submit the ACALCI 2015 abstract paper.
  • 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

  • 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

  • Literature review on the vessel-based lung segmentation
  • Make the MIA paper submission
  • Make the TBE paper submission
  • Make PhD thesis submission


Oct 27 - Oct 31


Nov 03 - Nov 07


Nov 10 - Nov 14


Nov 17 - Nov 21


Nov 24 - Nov 28


Dec 01 - Dec 05


Dec 08 - Dec 12


Dec 15 - Dec 19

  • End of project