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Chunk #5 — Method — DTI Data Processing and Probabilistic Tractography

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STRUCTURAL AND FUNCTIONAL CONNECTIVITY IN POSTTRAUMATIC STRESS DISORDER: ASSOCIATIONS WITH FKBP5.
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Correction for head motion and eddy current distortion was performed for data from each participant using an automated affine registration algorithm. Both diffusion-weighted and T1 images were skull-stripped using the FSL brain extraction tool(33). FA maps were generated using the DTIfit in the FMRIB Diffusion Toolbox. Markov Chain Monte Carlo sampling was used to calculate within-voxel probability density functions of the principal diffusion direction using FSL’s BEDPOSTX tool, which also accounts for the possibility of crossing fibers within a voxel (21). Probabilistic fiber tracking was conducted with PROBTRACKX implemented in FSL; this method repeatedly samples the distribution at each voxel to produce ‘streamlines’ that connect voxels from selected seed regions (5000 streamline samples, .5 mm step length, curvature threshold = .2). A mask of the cingulum, created using the JHU White Matter Tractography Atlas (34), was used as an anatomical waypoint to constrain probabilistic tracts; a separate exclusion mask was created to further eliminate the likelihood of pathways in irrelevant white matter tracts, gray matter regions and CSF. Hippocampus and ACC masks were used as seed regions for the tracts,