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Dear FSL Experts, I've been working on generating a structural connectivity matrix using diffusion data. To do so, I've been first creating 264 seed points (spherical roi's of radius 5) based on Powers et. al 2011 parcellation scheme, and then running probtrackx on the multiple masks condition (no termination, exclusion, or waypoint conditions) with -omatrix1 (seed by seed connectivity) and with standard parameters. This gives me a 264 by 264 whole brain structural connectivity matrix (once I average over the voxel). When I looked however, only local projections were uncovered, and basically nothing off of the diagonal (in the fdt_network_matrix) showed anything. Does anyone have any suggestion for identifying where I went wrong or on how to generate the structural connectivity matrix that will actually identify projections? Thank you for your help! Levi Solomyak