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