Hello,
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.
In theory this should give me a 264 by 264 whole brain structural connectivity matrix (once I average over the voxel), which I should be able to pull out by looking at the fdt_matrix1.dot file. When I looked however, no real projections were uncovered.
Does anyone have any suggestion for identifying where I went wrong or on how to generate the structural connectivity matrix? One thought is that my seed regions have too much gray matter in them and that maybe I should dilate the white matter masks first.
Have other people encountered a similar problem?
Thank you in advance for your help!
Levi
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