View source for 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: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 1249 Boylston Street]
* Friday meeting location: [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. 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
** SLC meeting 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
{|
|<gallery perrow="3" heights="200px" widths="300px">
Image:oscar_snr.jpg|'''Oscar'''
Image:tommy_snr.jpg|'''Tommy'''
Image:louis_snr.jpg|'''Louis'''
</gallery>
|}
* 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 at the initial time-point: [[October 07 2009 Meeting: VT-NAMIC Data review summary]]
** Discussed AC-PC usage module. Agreed possibly not helpful, since it does not align AC-PC line and midline between subjects, only straightens the AC-PC to be horizontal, and midline to be vertical. Manual alignment is needed prior to this to reliably locate AC and PC.
** Considering the data review (mis-alignment of the subjects in atlas; presense of bias; severe noise problems with some of the subject, while better data is available for the same subjects), and availability of the new tools (BRAINSFit robust up to BSplines, N3 bias correction in Slicer does good job -- can improve bias and registration) agreed that the atlas construction must be revisited
** Agreed on the conventions how to choose and load the data, all 10 subjects prepared in NRRD from the raw DICOM data, visually inspected for errors [[October 07 2009 Meeting: VT-NAMIC Data load protocol and comments]]
** Sandy suggested to include anisotropic diffusion into the atlas construction and segmentation workflow. EM Segmenter result can possibly be improved by adjusting the MFA parameter. 
** Earlier comments from Kilian: bias correction can possibly be improved by increasing the number of EM iterations, changing the width and sigma (the last two ones are not accessible from GUI as of now).
** Ginger's laptop has problems running Slicer -- had to apply updates and are in the process of recompiling Slicer -- should be ready by Thursday
* Separate page for the [[VT-NAMIC Workflow Slicer-related issues]] -- to be revised and submitted as bug reports

* Oct 8
** Work on the revised atlas workflow: [[October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow]]
** New discoveries and updates for the data review: [[October 07 2009 Meeting: VT-NAMIC Data review summary]]
** Slicer is working on Ginger's laptop -- needed to switch off desktop effects
** To be discussed on Oct 9: [[Oct 08 2009 meeting: schedule for Oct 9]]

== Attendance ==

Open to all interested parties:

#Chris Wyatt
#Ginger Li
#Ron Kikinis
#Sandy Wells
#Andriy Fedorov

== References ==
* 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/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.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]
* [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