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Dear Group, I think the -f flag may have contributed to a bigger difference in the running time of probtrackx than I had originally realized...(as you folks suggested in the first place) Duhhh...maybe the exclusion mask was not responsible at all for the running time difference, maybe it was just my failure to notice that the DATE STAMP was different on fdt_paths...not just the time... I'm so mortified and I'm rerunning the analysis without -f now to verify my new theory...very sorry for wasting your time : ( ======================== Since I just reran probtrackx on equivalent data with equivalent commandlines, I compared the outputs, and they seem to be different. I am deeply suspicious that my inability to tell time has something to do with this too, but, just in case it doesn't...is there any reason you can think of for this? Thankyou for your patience.. Dianne Post-Patch: dpat% cat cst_l/probtrackx.log probtrackx --network --mode=seedmask -x cst_l/masks.txt -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir -f --opd -s Bed.bedpostX/merged -m Bed.bedpostX/nodif_brain_mask --dir=cst_l dpat% fslstats cst_l/fdt_paths.nii.gz -V -R 7840 137961.171875 0.000000 61377.000000 =================================== Pre-Patch: dpat% fslstats cst_l_back/fdt_paths.nii.gz -V -R 9803 172504.250000 0.000000 108753.000000 dpat% cat cst_l_back/probtrackx.log probtrackx --network --mode=seedmask -x cst_l_f/masks.txt -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir -f --opd -s Bed.bedpostX/merged -m Bed.bedpostX/nodif_brain_mask --dir=cst_l_f --------------------------------------------- -Dianne -- Dianne Patterson, Ph.D. [log in to unmask] ERP Lab University of Arizona 621-3256 (Office)