Hi FreeSurfers, I would like to use cortical surface ROIs generated in FreeSurfer to perform inter-regional WM tractography using FSL's probtrackx tool. My understanding is that start seeds and targest are typically defined by mapping the labeled gray-white surface to the DTI volume. I.e., voxels that intersect the surface are given labeled with the appropriate ROI. Is that the case? If so, it seems like this could potentially result in false negatives if the alignment between the surface and a particular voxel is particularly troublesome. For instance, if an intersected voxel (call this Voxel 1) is primarily within the cortex, the adjacent voxel deeper within the white matter (Voxel 2) might have a low FA. In this case, a tract starting from Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA threshold. No tracts would therefore be generated from Voxel 1. Alternatively, tracts on their way to this ROI from other other regions might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this is, particularly given typical DTI resolution. Has anyone else had this concern or looked into to the likelihood of it occurring.
One solution that should be fairly easy to implement would be to label both the voxels that intersect the gray-white surface and their nearest neighbor within the white matter. Has anyone attempted this? Many thanks for any feedback you can provide. Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Cognitive and Neural Systems Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755
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