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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.