Difference between revisions of "Events:VT-NAMIC-NCBC-Collaboration-meeting-2009"
From NAMIC Wiki
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* Measuring alcohol and stress interaction [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NCBC Collaboration page] | * Measuring alcohol and stress interaction [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction NCBC Collaboration page] | ||
* [http://wiki.na-mic.org/Wiki/index.php/Atlas-to-subject_registration_with_FSL_and_Diffeomorphic_Demons,_for_EM_segmentation. Atlas construction workflow], put together by Ginger prior to the meeting | * [http://wiki.na-mic.org/Wiki/index.php/Atlas-to-subject_registration_with_FSL_and_Diffeomorphic_Demons,_for_EM_segmentation. Atlas construction workflow], put together by Ginger prior to the meeting | ||
| − | * [http://wiki.na-mic.org/Wiki/index.php/On_the_performance_of_Slicer_2_and_Slicer3_EM_segmentation_modules Slicer 2 vs. Slicer 3 EM Segmentation performance qualitative comparison], completed by Ginger prior to the meeting | + | * [http://wiki.na-mic.org/Wiki/index.php/On_the_performance_of_Slicer_2_and_Slicer3_EM_segmentation_modules Slicer 2 vs. Slicer 3 EM Segmentation performance qualitative comparison], completed by Ginger prior to the meeting; also as a [http://www.na-mic.org/Wiki/index.php/Current_atlas_construction_workflow table] |
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Atlas construction workflow] off BSL web site | * [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Atlas construction workflow] off BSL web site | ||
* [http://www.na-mic.org/Wiki/index.php/Vervet_MRI_registration Evaluation of BRAINSFit performance on atlas-to-subject vervet registration], completed by Andrey prior to the meeting | * [http://www.na-mic.org/Wiki/index.php/Vervet_MRI_registration 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 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf] | * 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 [http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.unc.edu%2F~styner%2Fpublic%2FMyPapers%2Fpapers%2FMedical%2520Imaging%25202007%2520Image%2520Processing%25202007%2520Styner-1.pdf&ei=DubDSt3AAciwlAfJp5TwBA&usg=AFQjCNGojUvBkh6TwbS0vJ9X7OEFLDFxqQ&sig2=wHgXTrdAXzUC5DuL_C7CCQ pdf] | ||
* [http://wiki.na-mic.org/Wiki/index.php/Proposed_revised_atlas_construction_workflow Revised atlas construction workflow proposal], completed by Andriy Fedorov, communicated to Ron, Sandy, Sylvain Jaume, discussed with Sandy, all prior to the meeting | * [http://wiki.na-mic.org/Wiki/index.php/Proposed_revised_atlas_construction_workflow Revised atlas construction workflow proposal], completed by Andriy Fedorov, communicated to Ron, Sandy, Sylvain Jaume, discussed with Sandy, all prior to the meeting | ||
Revision as of 23:03, 5 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
- 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
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
