You could try this:
/home/matt/fsl4.1/bin/probtrackx -x
/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/lpcc.nii.gz -V
1 -l -c 0.2 -S 2000 --steplength=0.5 -P 5000
--avoid=/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/exclude
.nii.gz --forcedir --opd -s
/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/./merged -m
/home/matt/TRIO/090522/DICOM/09052216/41270000/dti2.bedpostX/./nodif_brain_m
ask --dir=l_cingulate --waypoints=l_cingulate/waypoints.txt
I removed what appeared to be some typos in your commandline, and -f and
-modeuler, neither of which I have found to improve your results (see
previous discussions of -f for why there is a better way of accomplishing
this).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Matthew Hoptman
Sent: Monday, June 01, 2009 12:02 PM
To: [log in to unmask]
Subject: Re: [FSL] waypoint mask doesn't work?
Hi Saad,
No, I mean I don't get an fdt_paths.nii.gz image at all!
I didn't use the -f option in my original tractography (I haven't used the
command line thus far -- what I sent previously was the contents of the
probtrackx.log from my waypoints analysis). In my original attempt, I put a
seed in left posterior cingulum, along with a midline exclusion mask, and
got a
beautiful result that wraps around the callosum as it should. I put a
waypoint
seed in the middle of the A-P extent of the cingulum hoping to constrain the
anlaysis, and that's where I'm stuck (nb, I had used the same exclude mask
in
both analyses, I tried the waypoint analysis without the exclude mask, but
still
no luck).
I just verified that the tract from the seed roi passes directly through the
waypoint mask, so that shouldn't be the problem either.
Best,
Matt
PS. My sequence should be fine: 30 directions, 7 b=0 images, b=0, 800.
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