I would make everything in the HCP’s space and use the caret --meshspace option.
Matt.
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.
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