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Thank you Michiel, for your suggestion r probtrackx2. I have tried the probtrackx2 command as you suggested above both with and without the --opd flag. Neither is anywhere close to the probtrackx run on the same tract. The probtrackx run retains a lot of voxels in the two endpoint masks...but probtrackx2 does not retain them (it goes to 0 or 1 voxel retained pretty quickly). I am surprised to find that probtrackx2 is so different, and that I have apparently lost functionality in probtrackx2 vs probtrackx. I suppose I could continue using probtrackx, but I'd love to understand what is going on here. Thanks for your time, Dianne On Fri, Feb 2, 2018 at 3:33 AM, Michiel Cottaar < [log in to unmask]> wrote: > 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]> 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] <[log in to unmask]> > or > [log in to unmask] > University of Arizona > Speech and Hearing Science 314 > 1131 E 2nd Street, Building #71 > <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371&entry=gmail&source=g> > (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 > ============== > > >