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Ok, I see. Does it print any message? ... I mean probtrackx2 On 3 February 2018 at 17:59, Dianne Patterson <[log in to unmask]> wrote: > I should also note that probtrackx2 finishes in just a few minutes...as if > it isn't really engaging in the task. > -Dianne > > On Sat, Feb 3, 2018 at 3:41 PM, Dianne Patterson <[log in to unmask]> > wrote: > >> I see what you mean, I am iterating back and forth between the 2 seed >> masks...I must have grabbed different iterations for my last example (which >> makes things harder for you...sorry). Here is the first iteration of each >> of them: >> >> probtrackx --network --mode=seedmask -x subjectrois/atl_r_diff_bin_csf -l >> -c 0.2 -S 2000 >> --steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf >> --forcedir -f --opd >> -s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask >> --dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t >> >> fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V >> 1791 19070.572266 >> ============================== >> probtrackx2 -x subjectrois/atl_r_diff_bin_csf -l -c 0.2 -S 2000 >> --steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf >> --forcedir -f >> -s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask >> --dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t >> >> fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V >> 2 21.296003 >> ============================= >> Thank you for spending time helping me with this. >> >> -Dianne >> >> >> On Sat, Feb 3, 2018 at 1:08 PM, Moises Hernandez <[log in to unmask]> >> wrote: >> >>> mmmm are you using the same seed mask? >>> >>> -x subjectrois/frontal_orbital_r_diff_bin_csf >>> -x subjectrois/atl_r_diff_bin_csf >>> >>> On 3 February 2018 at 15:02, Dianne Patterson <[log in to unmask]> wrote: >>> >>>> Thank you Moises, >>>> Here is the command I am running in probtrackx: >>>> >>>> probtrackx --network --mode=seedmask -x subjectrois/frontal_orbital_r_diff_bin_csf >>>> -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 >>>> --stop=subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir *-f* --opd >>>> -s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask >>>> --dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t >>>> >>>> I found I cannot simply call probtrackx2 with the same flags, and I've >>>> tried various alternative options based on the gui and reading. I am >>>> primarily interested in the seeds-to-target masks that get generated. >>>> Clearly I'm doing something very wrong. Here is one of the options I tried >>>> in probtrackx2 (but all of the options I've tried have similar results): >>>> >>>> probtrackx2 -x subjectrois/atl_r_diff_bin_csf -l -c 0.2 -S 2000 >>>> --steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf >>>> --forcedir -f --opd -s dwi/Bed.bedpostX/merged -m >>>> dwi/Bed.bedpostX/nodif_brain_mask --dir=dwi/unc_r_bip >>>> --targetmasks=dwi/unc_r_bip/targets.txt --os2t >>>> >>>> (In both cases I have shortened the paths in this email to make the >>>> commands easier for us to read) >>>> >>>> result using probtrackx command above: >>>> fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V >>>> 1791 19070.572266 >>>> >>>> result using probtrackx2 command above: >>>> fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V >>>> 2 21.296003 >>>> >>>> What am I missing? >>>> >>>> Thanks so much, >>>> >>>> Dianne >>>> >>>> >>>> On Sat, Feb 3, 2018 at 12:25 PM, Moises Hernandez <[log in to unmask]> >>>> wrote: >>>> >>>>> Dianne, probtrackx2 has not lost any functionality (what function do >>>>> you think it has lost?). >>>>> It is the opposite, it has added functionality. >>>>> >>>>> What exact commands (probtrackx & probtrackx) are you using for >>>>> comparing the results? >>>>> >>>>> Moises. >>>>> >>>>> On 3 February 2018 at 14:10, Dianne Patterson <[log in to unmask]> >>>>> wrote: >>>>> >>>>>> 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 >>>>>>> ============== >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >