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--lrmask is associated with --omatrix2. What are you trying to use probtrackx to do? Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Corina Melzer Sent: Thursday, November 04, 2010 6:31 AM To: [log in to unmask] Subject: [FSL] ProbtrackX lrmask Hi, I'm using probtrackx for tractography and I am wondering about the probtrackx option --lrmask, for which I couldn't find any documentation. I know it is for defining a low resolution mask, if seed space is in high resolution. But what is it really doing and why is it necessary? I'm asking this, since when starting tractography using our data I need to specify this low-res mask. Otherwise I'll get an error message: "Image Exception: #22 :: Failed to read volume". By the way it was hard to figure out, what the real problem behind this error was. Our seed space is 160x200x160 (1mm) and diffusion space is 182x128x72 (1.7mm). I use the following command for tractography: probtrackx -s <bedpost_dir>/merged -m <bedpost_dir>/nodif_brain_mask --xfm=anat2diff.mat -x fdt_coordinates.txt --seedref=./t1.brain --opd -P 5000 --loopcheck --forcedir --omatrix2 --dir=connect --s2tastext --mode=simple [--lrmask=./lrmask_5mm.nii.gz] Do you additionally have any suggestions concerning the resolution of this lrmask and how does this influence my tractograms? Thanks for your help. Corina