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Dear All I am trying to run probtrackx 2 from cortical regions generated by freesurfer. I've followed the instruction in the wiki for label2surf (i think!) but was wondering if there was a way to visually check the .gii files this generates which can be used for tracking? I have been trying to use the freesurfer function mri_surf2vol to convert the .gii files to .nii.gz files for illustrative purposes. This command runs but produces blank (empty) .nii.gz files. I've been in discussion with the freesurfer mailing list and they've suggested the problem is with the label2surf function, as the .gii files I've produced so far don't load onto freeview or tkmedit. I think I followed the commands properly having searched this forum. For example, to generate a surface file for the right precentral gyrus: mris_convert lh.white lh.white.asc echo lh.precentral.label > _ left_precentral.txt label2surf -s lh.white.asc -l left_precentral.txt -o left_precentral.gii. Probtrackx seems to accept these as files for seeding and running seeding from the leftprecentral region with a waypoint in the pons I get a reasonable corticospinal tract , though this seems to not extend all the way up to the white/grey interface but instead only to the centrum semiovale. I've used the rawavg.mgz file (converted to rawavg.nii.gz) as the seed reference, and I'm happy with the transformations to diffusion space (the inverses take ROI from diffusion to the rawavg.nii.gz perfectly). I would be very grateful for any guidance that could be offered. Dan