Events:VT-NAMIC-NCBC-Collaboration-meeting-2009

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Logistics

  • Andriy Fedorov and Ginger Li: work on pre-meeting agenda Wed-Thu October 7-8, 2009
  • All participants meeting: Friday, October 9, 2009, 9am-4pm (time is tentative, but room has been reserved, confirmed with Katie Mastrogiacomo)
  • Wednesday and Thursday location: 1249 Boylston Street
  • Friday meeting location: 1249 Boylston Street, 2nd floor conference room

Goals

  • To be completed or partially completed prior to the meeting by Andriy Fedorov and Ginger Li (Oct 7-8):
    • Provide necessary user- and developer-level Slicer training for Ginger
    • Understand the currently used processing workflow
    • Confirm reproducibility of the processing steps between VT and SPL
    • Document the processing steps as precisely as necessary for reproducibility and cross-validation of the results (wiki page)
  • To be completed during the meeting
    • Review and confirm the correctness of the workflow based on the wiki documentation (Chris, Ron and Sandy)
    • Review the available data and current segmentation results
    • Discuss action timeline for the remaining part of the funded project period
      • Potential for segmentation validation using cryo-histology (Chris can show some results of reconstructed 3D cryo-histo volumes)
      • Potential for cortical thickness measures / integration with Caret or freesurfer
    • Discuss publication plans

Agenda

  • Review, discuss and finalize the processing workflow (to be discussed and documented by Andriy Fedorov and Ginger Li prior to the meeting Oct 7-8)
    • atlas construction
    • image pre-processing
    • registration
    • segmentation
  • Review currents results
    • Tommy and Louis images appear to have bad quality. Ron recommends not to use these subjects for atlas construction
  • Identify Slicer components of the workflow that are ... working, broken, missing

Schedule

  • Wednesday, Oct 7 plans:
    • Walk through the segmentation workflow with EM Segmenter, verify scene saving, usability (Ginger)
    • Document the current segmentation problems, prepare for discussion with Sandy
    • 4pm: Meet with Sandy at Thorn to discuss current EM Segmenter results
    • Install/verify installation of Slicer and related modules (BRAINSFit, N3MRILightCLI) (Andrey)
    • Using and developing Slicer modules/extensions (Andrey)
    • Using BRAINSFit (Andrey)
    • AC-PC module usage for pose alignment (Ginger)
    • Data transfer (images + segmentations)
    • Aftenoon: Ron stops by to review progress (?)
  • Friday, Oct 9, 9am (earlier?): Ron, Sandy, Ginger, Andrey meet at Boylston conference room to start discussion
  • 10am: Chris' flight arrives at Logan
  • 1pm: Chris gives a journal club talk at 1249 Boylston conference room
  • 7pm: Chris' flight departs from Logan

Progress

  • Oct 7
  • Reviewed available data
    • The issue with noise in Tommy and Louis resolved: we do not know how the NIFTI images we used before for Tommy and Louis were obtained -- the DICOM data has much better noise characteristics
    • Angio sequence (right name?) has apparently been used for some (7 out of 10) subjects
    • Strange artifact is observed in the occipital lobe for all subjects. Ron, Sandy, Sota Oguro (SPL radiologist) cannot explain the origin.
    • Noticeable bias field in the atlas is observed by Ron
    • Significant mis-alignment of some subjects with the template subject after FLIRT registration is confirmed
    • Ringing artifacts for some (few) subjects

Attendance

Open to all interested parties:

  1. Chris Wyatt
  2. Ginger Li
  3. Ron Kikinis
  4. Sandy Wells
  5. Andriy Fedorov

References