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Thanks a lot. It's solved. Regards, Nabin On Fri, May 29, 2015 at 5:45 PM, Moises Hernandez <[log in to unmask]> wrote: > Hi Nabin, > > try to change: > --xfm /gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/xfms/ > diff2standard.mat > with > --xfm*=*/gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/xfms/ > diff2standard.mat > > Best, > Moises. > > > On 29 May 2015 at 16:39, Nabin Koirala <[log in to unmask]> wrote: > >> Dear experts, >> >> I am trying to run the following command for the probtrackx2 but I am >> getting the error saying >> >> --xfm: Missing non-optional argument ! >> >> I checked in the forum and i saw the solution saying label file needed to >> be converted to surface file. But in my case I am not using label file from >> freesurfer , the masks.txt in my case contains the path of ROIs masks >> needed. And also when I don't put the --xfm option the process runs without >> any error. >> >> Your suggestion would be really helpful. >> >> probtrackx2 --network -x >> /gpfs/fs1/home/nkoirala/trial_data/G_Babar/dti.bedpostX/masks.txt >> --targetmasks=/gpfs/fs1/home/nkoirala/trial_data/G_Babar/dti.bedpostX/masks.txt >> -V 1 --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 >> --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s >> /gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/merged -m >> /gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/nodif_brain_mask --xfm >> /gpfs/fs1/home/nkoirala/Gesunde/HC001.bedpostX/xfms/diff2standard.mat >> --dir=/gpfs/fs1/home/nkoirala/Gesunde/HC001/tracktography >> >> Thank you. >> >> Regards, >> Nabin >> >> >