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 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:

• Update color look up table http://wiki.na-mic.org/Wiki/index.php/Lung_Segments_Color_Map
• Regenerate the models for the dataset
• Literature review on automated segmentation of lung segments. http://lola11.com/
• Check the vessel segmentation tool in the Cardiac Agaston tutorial with Jessica http://wiki.na-mic.org/Wiki/index.php/CardiacAgatstonScoring_TutorialContestSummer2014
• Try airway segmentation on Slicer 4 with lung project dataset.

[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

Dec 15 - Dec 19

• End of project