DBP:Andy Saykin visit BWH December 14 2005

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Home < DBP:Andy Saykin visit BWH December 14 2005


  • Dartmouth: Andy Saykin, John West, Bob Roth (others?)
  • BWH: Steve Pieper, Sandy Wells, Wendy Plesniak (fMRI), Haiying Liu (fMRI), C-F Westin (DTI), Raul San Jose (DTI).


  • fMRI
    • Test new Slicer fMRI package with Dartmouth Data (2 motor cases)
    • Compare results to SPM
    • Discussion on where to improve fMRI package in Slicer after testing
  • DTI
    • Discussion of what new improvements/features in Slicer 2.6 DTI
    • Discussion of improvements still needed in DTI package (eddy current correction, scale factors, etc.)



  • Dartmouth people arrive 10am
  • 10:00 - 11:00 -- DTI meeting with Marty and Schiz group
  • 11:00 - 12:00 -- fMRI Phase I - Wendy, Haiying, Carsten
    • copy Dartmouth data
    • overview of software and new features
    • start analysis with new data
  • 12:00 - 1:15 -- Lunch (with Marty and anyone)
  • 1:15 - 1:45 -- EM Atlas Classifier (Kilian Pohl)
    • test slicer2.6 version on dartmouth datasets
    • discuss plans for AHM
  • 1:45 - 3:00 -- fMRI Phase II - Wendy, Haiying, Steve, Sandy, Carsten
    • review results, statistics, blobs, models
  • 3pm LMI meeting: Present recent DTI developments and discuss open issues
    • Lauren O'Donnell will show some recent developments relating results from fiber clustering and fMRI
    • David Banks will show new software visualizing Lauren's fiber clustering results

Meeting Notes (John D. West)

  • 10:00 - 11:00 -- DTI meeting with Marty and Schiz group
    • Presentation on fiber tracking of arcuate fasciculus (AF)
      • Background on function of AF.
      • Description of difficulty in fiber tracking of AF
        • 2x2x2.4mm EPI DTI - tracts in AF do not fully track in EPI based sequences
        • LSDTI - line scan DTIs perform better but are much longer (30 min sequences)
      • Discussion ongoing about whether to go with line scan or EPI sequences
  • 11:00 - 12:00 and 2:00 - 3:00-- fMRI - Wendy, Haiying, Carsten
    • Discussed progress of fMRI analysis module
      • Event related analyses have been implemented
      • Results from first Dartmouth control using new module seem much improved
      • Ability to output clusters to label maps and then get statistics within each cluster
    • Discussed improvments to be made
      • Add batch processing feature
      • Add ability to save model settings
      • Need to be able to separte deactivation clusters in label map from activation clusters when doing statistics
      • Ability to do group analyses on data - general change to slicer
  • 1:15 - 2:00 -- EM Atlas Classifier (Kilian Pohl)
    • Joint segmentation and registration - large improvement over registration to atlas then segmenting
    • Is usable with any atlas
    • Need SPGR and T2 (aligned) to perform segmentation
    • Potential to auto segment 30+ structures with current atlases though some issues still need testing and tweaking
  • 3pm - ~4pm LMI meeting: Present recent DTI developments and discuss open issues
    • Lauren O'Donell - fiber clustering and fMRI
      • Development of program in slicer to cluster individual fiber tracts into groupable clusters - automatic
      • Tools to further group clusters into major fiber tracts - manual
      • Shown on test case on tumor patient - how fiber tracts and fMRI activation clusters interacted with tumor
      • Sent reference to Lauren on classification of white matter by FA value (WM>0.2 FA) - hopefully will assist in project (Ref: Pierpaoli et al., Radiology, 1996. DTMRI of the Human Brain.)
    • David Banks - visualization of fiber clustering from Lauren
      • Using global lighting to improve realistic visualization of fibers
      • Rendering computationally time consuming - but tools available to convert this to 3D movie for later viewing in real time
    • Gordon Kindlmann - Eddy Current correction
      • Correction of eddy currents using a moment based approach - no need for reference scan (e.g. Mean DWI image) to correct disstortions
      • Tested on first dartmouth control DTI with good success
      • Currently working on polishing program for Slicer 2.6
      • Measurement of moments could potentially be used for DTI QC
  • 4pm on - Bob Roth and John West discussion with Steve Pieper on possible Slicer improvement and new features in Slicer 2.6
    • Possible improvements to make
      • Global save - option to save all images in scene at one time
      • Smaller pointer for tracing - arrow obstructs view while tracing and is not as accurate
    • New improvements in Slicer 2.6
      • Keyboard commands for tracing
        • To change colors on the fly
        • Delete previously drawn lines
        • Hold shift key to have other two views follow tracing in view being editted
      • Joint smoothing of multiple models
      • Save all models function
      • Also learned about color map editting and saving (current commands)
    • Also discussed a couple of potential bugs (in bug tracker), but could not reproduce - John West and Bob Roth will keep an eye on these to see if the are present in Slicer 2.6

Huge thanks to Marty Shenton and her group for having us visit.