Update: I ran the following at the command line and it worked fine. I'm
confused, though because the command shouldn't have been too different
from what I ran in the gui. Maybe the program didn't properly read the
waypoints.txt file. In the command that worked (below), I explicitly specified
the waypoints image.
/home/matt/fsl4.1/bin/probtrackx --mode=seedmask -
x /home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/lpcc.nii.
gz -V 1 -l -f --modeuler -c 0.2 -S 2000 --steplength=0.5 -P 5000 --
avoid=/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/exc
lude.nii.gz --forcedir --opd -
s /home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/./merge
d -
m /home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/./nodif_
brain_mask --dir=l_cingulate --
waypoints=/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpost
X/lacing.nii.gz -o test_way
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