The diffusion data are in the subjects native (T1w) space. You just need to use surfaces that are also in that space (e.g. the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k). I would recommend using the white surface for counting and the pial surface for stopping.
As for the exact command, I would use the link I posted to figure that out as I haven’t tried to do this yet. Also, perhaps one of our diffusion colleagues might post some help too. Peace, Matt. From: Max Bertolero <mb3...@seas.upenn.edu<mailto:mb3...@seas.upenn.edu>> Date: Tuesday, August 1, 2017 at 2:10 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2 Thanks! Right, the parcellation stuff seems pretty easy, but how to call the probtrackx2 with those label files is a bit trickier. Do you have an example FSL command for a HCP subject? I can’t really figure out what I need to do, and what HCP has already done. For example, do any transforms need to be calculated? Do I just need the subject surface to fsaverage transform? Thanks again, Max On Aug 1, 2017, at 2:51 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: You can use wb_command -cifti-separate to get GIFTI label files out and then use https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Max Bertolero <mb3...@seas.upenn.edu<mailto:mb3...@seas.upenn.edu>> Date: Tuesday, August 1, 2017 at 1:40 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2 If I want to use a fslr32k (or fsaverage) parcellation as seeds for probtrackx2, does anyone know how do this on the command line? For example, I would want to use this fsLR32k parcellation: https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/HCP/fslr32k/cifti/Schaefer2018_400Parcels_17Networks_order.dlabel.nii Thanks! Max Bertolero, PhD _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users