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

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

Oscar Tommy Louis

• 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

Tommy, DICOM Louis, DICOM

• • Angio sequence (right name?) has apparently been used for some (7 out of 10) subjects

Calvin axial showing vessel and volume rendering of vasculature

• • 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

• Measuring alcohol and stress interaction NCBC Collaboration page
• Atlas construction workflow, put together by Ginger prior to the meeting
• Slicer 2 vs. Slicer 3 EM Segmentation performance qualitative comparison, completed by Ginger prior to the meeting; also as a table
• Atlas construction workflow off BSL web site
• Evaluation of BRAINSFit performance on atlas-to-subject vervet registration, completed by Andrey prior to the meeting
• M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8 pdf
• Revised atlas construction workflow proposal, completed by Andriy Fedorov, communicated to Ron, Sandy, Sylvain Jaume, discussed with Sandy, all prior to the meeting