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Hi Dianne, I suspect that the difference in behaviour is not due to the --mode or even the --network mask, but in the original probtrackx you specify a set of classification targets (through the flags: " --targetmasks=sub-5167/dwi/unc_r_bip/targets.txt --os2t “), however in the new command you choose to output only the path distribution (--opd flag) What happens if you run the probtrackx2 with the same flags as the original probtrackx command, but without the —network or --mode option: probtrackx2 -x sub-5167/subjectrois/frontal_orbital_r_diff_bin_csf -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=sub-5167/subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd -s sub-5167/dwi/Bed.bedpostX/merged -m sub-5167/dwi/Bed.bedpostX/nodif_brain_mask --dir=sub-5167/dwi/unc_r_bip --targetmasks=sub-5167/dwi/unc_r_bip/targets.txt —os2t Good luck, Michiel On 1 Feb 2018, at 01:30, Dianne Patterson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear dti experts: I was hoping to move from probtrackx to probtrackx2, but it seems more complex than I had anticipated: I can run this command: probtrackx --network --mode=seedmask -x sub-5167/subjectrois/frontal_orbital_r_diff_bin_csf -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=sub-5167/subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd -s sub-5167/dwi/Bed.bedpostX/merged -m sub-5167/dwi/Bed.bedpostX/nodif_brain_mask --dir=sub-5167/dwi/unc_r_bip --targetmasks=sub-5167/dwi/unc_r_bip/targets.txt --os2t probtrackx2 -x sub-5167/dwi/unc_l_bip/masks.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --stop=sub-5167/subjectrois/unc_l_inv_mask_diff_bin_csf.nii.gz --forcedir --opd -s sub-5167/dwi/Bed.bedpostX/merged -m sub-5167/dwi/Bed.bedpostX/nodif_brain_mask --dir=sub-5167/dwi/unc_l_bip --------------------------------------------- probtrackx2 does not support --mode=seedmask Is there some equivalent? In addition, if I remove --mode=seedmask, probtrackx2 complains about --network. When I remove that as well, probtrackx2 behaves very differently than the original probtrackx command. I have tried probtrackx2 with and without the bolded flags --onewaycondition --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 (these are added to the command when I run with the gui). These also do not seem to make any difference. ============ I was running the original probtrackx command iteratively to look at the resulting size of the two grey matter masks. I don't understand how to replicate the original behavior with probtrackx2. Any help would be appreciated. Thanks, Dianne -- Dianne Patterson, Ph.D. Research Scientist [log in to unmask]<mailto:[log in to unmask]> or [log in to unmask]<mailto:[log in to unmask]> University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ==============