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Hi If your seed is a surface, then a streamline starting from a vertex on the surface won’t count as having traversed the surface unless it actually does step through it. The first step of the streamline will not produce a count. That may explain what you are seeing (provided I understood your question correctly) Saad On 30 Apr 2014, at 15:29, Scott Burns <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi FSL folks, I'm probtrack'ing between all Freesurfer cortical labels from the Destrieux atlas. For most of the probtrack runs, things look fine. That is to say, the most intense region of fdt_paths.nii.gz intersects strongly with seed area, which is to be expected. For some seeds however, the matrix_seeds_to_all_targets.nii.gz is completely blank and waytotal is 0. Even if none of the streamlines hit another target, since each streamline starts within one of the voxels of the seed (by definition), that initial "hit" should get counted towards the seeds row the output matrix, correct? I'm confident in my registrations, having overlaid both the structural image in diffusion space & the freesurfer orig image in diffusion space and verifying nothing strange occurred. For one of the bad seeds, I converted the FS label to a volume using mri_label2vol and applied the fs2dif transform. This volume overlays nicely on the non-diffusion weighted image. I've confirmed it doesn't intersect with the ventricles which I'm using as the --avoid argument. I generated GIFTI seeds with a loop along the lines of... for hemi in lh, rh mris_convert $hemi.white $hemi.white.asc for label in <labels> area = $hemi.$label.label seed = $hemi.$label.gii if the seed doesn't exist: echo $area > tmpfile label2surf -s $hemi.white.asc -o $seed -l tmpfile rm tmpfile Any help/explanation you can provide would be most appreciated! --Scott -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>