Difference between revisions of "Events:VT-NAMIC-NCBC-Collaboration-meeting-2009"
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** Noticeable bias field in the atlas is observed by Ron | ** 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 | ** Significant mis-alignment of some subjects with the template subject after FLIRT registration is confirmed | ||
+ | ** Ringing artifacts for some (few) subjects | ||
== Attendance == | == Attendance == |
Revision as of 23:54, 7 October 2009
Home < Events:VT-NAMIC-NCBC-Collaboration-meeting-2009Logistics
- 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:
- Chris Wyatt
- Ginger Li
- Ron Kikinis
- Sandy Wells
- 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