Difference between revisions of "Events:VT-NAMIC-NCBC-Collaboration-meeting-2009"

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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
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*  [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-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
  • 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:

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

References