1. Spring Meeting 2006 Tensor Atlas Morphometry BIRN Analysis, Visualization, and Interpretation

2. Goals from Miami  Provide tools to support testing of hypotheses related to in white matter morphometry Are depression-related white matter lesions more likely to occur in the area of certain tracts? (BELL Project) How does white matter vary among twin pairs compared to the general population? (VETSA Project)  Proposed Process Draw on JHU Tract Atlas experience  Use existing database  Have mBIRN researchers learn tools to expand atlas Draw on MGH Topographic White Matter Parcellation Use BWH Tensor Registration code to map atlases into subject space Integrate probabalistic white matter atlases into FreeSurfer to subdivide white matter (using both Structural and Diffusion Data

3. Topographic White Matter Parcellation Radiate Sagittal Bridging Individual fascicular divisions Anterior-Posterior ordered Parcellation Units Parcellated according to proximity to cortical Parcellation Units Geometric constructs for: -Sagittal Strata (superior, inferior, temporal, cingulum) -Corpus Callosum -Internal Capsule, Fimbrial-Fornix, Amygdalofugal Peripheral Deep

4. DTI - Interoperability  VETSA Datasets 35-Gradient DWI Acquisitions FreeSurfer Analysis of Each Subject ~300 Twin Pairs  Conversion of DWI data to NRRD has been completed

5. DTI Analysis - Atlas  JHU (Mori) Multi- Subject White Matter Labeled Tensor Atlas Available in Slicer (NRRD Format)  30 Subjects with full tensor data sets and tract label maps

6. Status and Outstanding Issues  JHU Tract Label Maps Not in Same Space as Average Tensor Revise strategy to register each atlas subject individually to target. Create probabilistic atlas in each target space.  FA-based Registration is Working and Should be Tested (more in later slides) Full Tensor Registration Code Not Robust, Further Algorithmic Development Needed Collaboration with NAC and NA-MIC. Others?  Integration with Topographic White Matter Parcellation TBD  Integration with FreeSurfer TBD

7. Batch registration in 3D-Slicer Using the AG-module Matthan Caan

8. Batch registration in 3D-Slicer Register a series of scans to an average brain Automatic procedure, no interaction needed. Can be done in the background or overnight. Coregistration of other scans is possible.

9. Using 3D-Slicer from the command-line Register a series of scans without any interaction: 1) Set up a virtual display Xvfb :2 -screen 0 800x600x16 2) Run Slicer slicer2-linux-x86 -y --no-tkcon --exec AGCommandLine avgFA.hdr FA_1.hdr tr_1.hdr ParamFile.tcl, exit -display :2 3) Repeat 2) for each scan to register using a simple script average scan individual scan scan to coregister parameter-file

10. Output Registered image will be saved. Registration parameters are stored for future use. 1.091 -0.0209 -0.0802 3.873 0.029 1.0827 0.1108 -19.732 0.063 -0.0933 0.8805 -2.277 0 0 0 1 affine transformation matrix non-rigid transformation file ( x, y, z, 3 )

11. Results (using lo-res data) before after affine after non-rigid atlas individual average of 60 registered subjects Individual resolution: 128*128*19 (2x2x6mm)