Hi,
I am trying to do a surface tracking (using FreeSurfer surfaces) as described
on the FDT webpage (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html), but I
am not sure if I do it right. I have generated and verified the
transformations, which seem to work. The problem I have is with the probtrackx
command arguments.
I would like to seed from a small volume in the hippocampus (defined as nii.gz)
and track to a surface (defined as label). Here is the command I used and which
results only to the hippocampal ROI:
probtrackx -x hippocamp_roi.nii.gz --mesh=../surf/lh.white.asc -l -c 0.2 -S
2000 --steplength=0.5 -P 5000 --forcedir --opd -s data.bedpostX/merged -m
data/nodif_brain_mask.nii.gz --dir=data.probtrackx --
xfm=anat/FS_2_FA_fnirt.nii.gz --invxfm=anat/FA_2_FS_fnirt.nii.gz --
seedref=anat/brainmask.nii.gz --mesh=../label/lh.frontalpole.label
Thanks for advice in advance,
Martin
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