Hi - this is weird: it looks like it’s trying to run a command that is different from the one you copied here: it’s trying to load a mask file where the path is missing a “/“ at the beginning. Are you sure that’s the exact command you have typed?

On 14 Jun 2016, at 09:10, André Schmidt <[log in to unmask]> wrote:

Dear experts,

I try to run probtrackx2 from the terminal but receive the following error:

[schandre@login10 ~]$ probtrackx2 --network -x /Applications/freesurfer/subjects/FEP039/mri/masks.txt -l --onewaycondition --omatrix1 -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /Applications/fsl/bedpostX_FEP_processed/bedpostX_FEP/039.bedpostX/merged -m /Applications/fsl/bedpostX_FEP_processed/bedpostX_FEP/039.bedpostX/nodif_brain_mask --dir=/Volumes/DTI/PROTRACKX_FEP/FEP039

Log directory is: /Volumes/DTI/PROTRACKX_FEP/FEP039

Running in network mode

Image Exception : #22 :: ERROR: Could not open image Applications/fsl/bedpostX_FEP_processed/bedpostX_FEP/039.bedpostX/nodif_brain_mask

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

Abgebrochen

I have no problem when running probtrackx from the GUI - do you know what is wrong with my command?

Many thanks for your help

André