Difference between revisions of "Core1"

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= Harvard =
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= Introduction =
  
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= Diffusion Data =
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* History: During MICCAI we (Ron Kikinis, Guido Gerig, Ross Whitaker, Polina Golland, Jim Miller, Tina Kapur, Martin Styner) discussed plans for the current year of NA-MIC. Given that this is the last year for the current participants in Core 3, we need to plan specific activities.
 +
* We will have an information exchange between Core 1 and Core 3 to discuss
 +
** a) clinical hypothesis and image analysis questions,
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** b) refined existing and new data sets related to a) and
 +
** c) refined and new algorithms available and ready to meet requirements of a) and b). Emphasis will be on the question what actions to take that will result in NA-MIC clinical application science papers especially w.r.t. the "low hanging fruits" discussed at the AHM.
  
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== 1.5T ==
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= Logistics =
  
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So far, we recruited and shared with Core 1: 40 chronic schizophrenics and 40 controls scanned with the old DTI LSDI protocol (1.7x1.7x5 mm, 6 directions, 1 baseline ).
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* The venue is the conference room on the second floor of our 1249 Boylston Street Facility [http://splweb.bwh.harvard.edu:8000/pages/directions/1249Boylston/Boylston-facility.html (directions)] in Boston on October 17 between 9.30am and 3pm.
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* Nancy Maxwell will be waiting downstairs to let you in the building. Call her at 617 525 6105 if she is not there.
  
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== 3.0T ==
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= Agenda =
  
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We started acquiring images on the 3T GE scanner. So far, we recruited and scanned 14 schizophrenics and 12 normal controls with SENSE EPI protocol (1.7x1.7x1.7 mm, 51 directions, 8 baselines). All these subjects have also 1x1x1 structural scans available. We will either make the complete set of 26 cases available or the 12 normal controls.
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* '''09.30am''' Begin
  
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<br /> The following scanner settings were used
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# Intro: Ron
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# Core 3: Discussion of newly available data (moderated by Martha Shenton & Andy Saykin)
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## [[Core1-3-meeting-2006/NewCore3Data|New Core 3 Data]]
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# Core 1: Discussion of algorithms and processing capabilities that candidates in this effort (moderated by Ross Whitaker & Guido Gerig).
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## [[NA-MIC_Internal_Collaborative_Projects#Diffusion_Image_Analysis|Diffusion Image Analysis]]
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## [[NA-MIC_Internal_Collaborative_Projects#Structural_Image_Analysis|Shape Analysis]]
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## [[NA-MIC_Internal_Collaborative_Projects#fMRI_Analysis|fMRI Analysis]]
  
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000001.SER Volume- 3D localizer
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* Identify specific analyses that should be initiated now. Specify teams, interactions and timetables (moderated by Ron Kikinis).
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* '''03.00pm''' Adjourn
  
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000002.SER ASSET- parallel calibration scan
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[[Media:NA-MIC_core-3.1-10-19-06.ppt|Core 3.1 Meeting slides, including list of short- and long-term projects]]
  
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000003.SER DTI Volume - R= 17000, TE Min= 78.3, FOV= 24.0, #Slices= 81, Resolution= 144x144, NEX= 1, directions 51, + 8 x T2, 1.7 mm X 1.7 mm X 1.7 mm
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= Ongoing Projects =
  
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000004.SER 3D FSPGR Axial, EDR, Fast, IvR, Asset - R= 7.5, TE= 3.0, FA=15 degrees, FOV= 25.6, 1 Phase FOV, Bandwith=15.63, Resolution= 256x256, Slice thickness 1
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* UF: 2 ROI tractography analysis with mean FA measures, doDTI ... submitted to Brain.
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* CF: previously defined ROIs, tractography with behavioral Stroop data, doDTI ... submitted to Archives of General Psychiatry.
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* AF: Registration of Susumu Mori’s atlas to our cases. Slicer Nonlinear FA to FA. No results. Need better registration.
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* CC: (1) Tractography. Fibers seeded in one slice CC ROI. Automated fiber clustering results in ROI color coded based on fiber clustering (Slicer, MIT Collaboration).
  
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000005.SER FSE T2 Axial - R= 6200, TE= 103, FOV= 25.6, 0.75 Phase FOV, ETL=16, Bandwith=31.25, Resolution= 256x256, Slice thickness 2mm, interleaved
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(2) Atlas based approach warping a CC subdivision to individual cases (UNC Collaboration).
  
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= Labelmaps =
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* ALIC: Work in progress. Tractography from anterior and posterior limb of the internal capsule. Slicer
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* STG: Mean FA, mean diffusivity within ROI defined on SPGR Slicer ... submitted to Biological Psychiatry.
  
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== Female caudate nucleus ==
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= Core 3 Wishes =
  
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We have new manually segmented labelmaps for the caudate nucleus of 32 women with schizotypal personality disorder and 29 normal control women. The caudate nucleus was delineated on coronal axis SPGR images (0.9375x0.9375x1.5 mm, 1.5T).
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* Registration:
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** Inter-subject diffusion to diffusion registration.
 +
** Intra- and inter-subject co-registration of structural, diffusion and functional MRI.
 +
* DWI/tensor/fiber smoothing.
 +
* Fiber asymmetry computation.
 +
* Fiber registration.
 +
* Tractography of white matter structures seeded in gray matter areas.
 +
* 3T artifact removal.
 +
* Segmentation of temporal lobe and basal ganglia.
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* Anatomical atlas for white and gray matter.
  
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See [http://pnl.bwh.harvard.edu/pub/papers_html/kooBiolPsych06.html Min-Seong et al.] for details.
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= List of Participants =
  
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= Previously available datasets =
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* Core 1
  
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For previously available datasets see [[DataRepository|DataRepository]].
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# Polina Golland, MIT
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# Guido Gerig, UNC
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# Ross Whitaker, UTAH
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# John Melonakos, Georgia Tech
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# Dennis Jen, MGH
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# Doug Greve, MGH
  
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<br />
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* Core 3
  
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= Dartmouth =
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# Martha Shenton, PNL
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# Marek Kubicki, PNL
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# Sylvain Bouix, PNL
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# Marc Niethammer, PNL
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# Andy Saykin, Dartmouth
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# John West, Dartmouth
  
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= 1.5T GE =
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* Other Cores
  
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== fMRI ==
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# Ron Kikinis, SPL
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# Randy Gollub, MGH and Core 5
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This is an EPI sequence acquired sagittally (3.75x3.75x5 mm)
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# Steve Pieper, Core 2 and 6
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# Brad Davis, Kitware
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'''Verbal Episodic Encoding/Recognition Task (event-related)''' - We have 14 subjects with schizophrenia and 9 normal controls.
 
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'''Auditory-verbal n-back Working Memory Task''' - We have 20 subjects with schizophrenia and 20 normal controls.
 
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== DTI ==
 
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This is an EPI sequence acquired axially (1.875x1.875x3 mm reconstructed to 0.9375x0.9375x3mm).
 
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Pre-processed and reviewed - We have 17 subjects with schizophrenia and 11 normal controls.
 
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Awaiting pre-processing and review - 15 subjects.
 
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Potentially 43 subjects total.
 
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== Structural ==
 
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All subjects have a hires SPGR 3D Volume (0.9375x0.9375x1.5 mm)
 
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= 3.0T Philips =
 
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Acquisition has now started. Trial case with DTI, fMRI Motor, and MPRAGE structural was incorporated in NAMIC tutorial.
 
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= Previously available data =
 
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For previously available datasets see [[DataRepository|DataRepository]].
 

Revision as of 13:21, 18 December 2006

Home < Core1

Introduction

  • History: During MICCAI we (Ron Kikinis, Guido Gerig, Ross Whitaker, Polina Golland, Jim Miller, Tina Kapur, Martin Styner) discussed plans for the current year of NA-MIC. Given that this is the last year for the current participants in Core 3, we need to plan specific activities.
  • We will have an information exchange between Core 1 and Core 3 to discuss
    • a) clinical hypothesis and image analysis questions,
    • b) refined existing and new data sets related to a) and
    • c) refined and new algorithms available and ready to meet requirements of a) and b). Emphasis will be on the question what actions to take that will result in NA-MIC clinical application science papers especially w.r.t. the "low hanging fruits" discussed at the AHM.

Logistics

  • The venue is the conference room on the second floor of our 1249 Boylston Street Facility (directions) in Boston on October 17 between 9.30am and 3pm.
  • Nancy Maxwell will be waiting downstairs to let you in the building. Call her at 617 525 6105 if she is not there.

Agenda

  • 09.30am Begin
  1. Intro: Ron
  2. Core 3: Discussion of newly available data (moderated by Martha Shenton & Andy Saykin)
    1. New Core 3 Data
  3. Core 1: Discussion of algorithms and processing capabilities that candidates in this effort (moderated by Ross Whitaker & Guido Gerig).
    1. Diffusion Image Analysis
    2. Shape Analysis
    3. fMRI Analysis
  • Identify specific analyses that should be initiated now. Specify teams, interactions and timetables (moderated by Ron Kikinis).
  • 03.00pm Adjourn

Core 3.1 Meeting slides, including list of short- and long-term projects

Ongoing Projects

  • UF: 2 ROI tractography analysis with mean FA measures, doDTI ... submitted to Brain.
  • CF: previously defined ROIs, tractography with behavioral Stroop data, doDTI ... submitted to Archives of General Psychiatry.
  • AF: Registration of Susumu Mori’s atlas to our cases. Slicer Nonlinear FA to FA. No results. Need better registration.
  • CC: (1) Tractography. Fibers seeded in one slice CC ROI. Automated fiber clustering results in ROI color coded based on fiber clustering (Slicer, MIT Collaboration).

(2) Atlas based approach warping a CC subdivision to individual cases (UNC Collaboration).

  • ALIC: Work in progress. Tractography from anterior and posterior limb of the internal capsule. Slicer
  • STG: Mean FA, mean diffusivity within ROI defined on SPGR Slicer ... submitted to Biological Psychiatry.

Core 3 Wishes

  • Registration:
    • Inter-subject diffusion to diffusion registration.
    • Intra- and inter-subject co-registration of structural, diffusion and functional MRI.
  • DWI/tensor/fiber smoothing.
  • Fiber asymmetry computation.
  • Fiber registration.
  • Tractography of white matter structures seeded in gray matter areas.
  • 3T artifact removal.
  • Segmentation of temporal lobe and basal ganglia.
  • Anatomical atlas for white and gray matter.

List of Participants

  • Core 1
  1. Polina Golland, MIT
  2. Guido Gerig, UNC
  3. Ross Whitaker, UTAH
  4. John Melonakos, Georgia Tech
  5. Dennis Jen, MGH
  6. Doug Greve, MGH
  • Core 3
  1. Martha Shenton, PNL
  2. Marek Kubicki, PNL
  3. Sylvain Bouix, PNL
  4. Marc Niethammer, PNL
  5. Andy Saykin, Dartmouth
  6. John West, Dartmouth
  • Other Cores
  1. Ron Kikinis, SPL
  2. Randy Gollub, MGH and Core 5
  3. Steve Pieper, Core 2 and 6
  4. Brad Davis, Kitware
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