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I would make everything in the HCP’s space and use the caret --meshspace option. Peace, Matt. From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Jonathan Bain <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Sunday, May 6, 2018 at 8:16 AM To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] Problems running probtrackx2 on HCP data Hello, I am running probtrackx2 and have encountered a problem, and I'm hoping that the FSL community might be able to help me out! My aim in running probtrackx2 is to identify a known white-matter bundle. I define endpoints in two cortical ROIs, and also require that the tracks traverse a white-matter waypoint. I am tracking twice: once seeding in cortical ROI-1 and terminating in cortical ROI-2, and once doing the reverse. The command I'm using looks something like this: probtrackx2 -s /path/to/subject/bedpostx/merged -m /path/to/subject/bedpostx/nodif_brain_mask.nii.gz -x /path/to/subject/freesurfer/surf/lh.roi1.gii --dir=/path/to/subject/outputDirectory --forcedir -o outputName --avoid=/path/to/subject/dtifit/exclusionMask.nii.gz --meshspace=freesurfer --seedref=/path/to/subject/freesurfer/mri/orig.nii.gz --xfm=/path/to/subject/dtifit/freesurfer2fa.mat --opd --onewaycondition--waypoints=/path/to/subject/ROIs/waypoint.nii.gz --stop=/path/to/subject/freesurfer/surf/lh.roi2.gii The bedpostx data and brain mask were downloaded from the HCP database. I created the cortical ROI gifti files using Freesurfer label files. I made the exclusion mask in Freesurfer space, and it's basically a white-matter mask in one hemisphere. I added the Freesurfer registration files in accordance to the FDT user guide<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#FreeSurfer_Registration>. For 75% of the subjects the tracking works as it should, but my problem is that the tracking isn't working for the remaining 25%. For the problematic subjects, it doesn't look like the tracks are going where they are supposed to; the tracks seem to originate in the seed region, proceed for a little bit, and then prematurely stop. If anyone has a suggestion, I'd love to hear it! Thanks in advance, Jonathan