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

• 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.
• 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

• 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. The b-values were found wrong.
• Prepare the DICTA 2014 abstract

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 15 - Sep 19

• Attend MICCAI 2014 conference in Boston

Sep 22 - Oct 03

• Two weeks' leave

Oct 06 - Oct 10

Lung project:

Graw 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

Todo List:

Update tutorial slides

Update color look up table

Try airway segmentation on Slicer 4 with lung project dataset.

Check the connectivity tool with Jessica.

Dec 15 - Dec 19

• End of project