You may need to add the —os2t option.
Cheers
Saad
> On 16 May 2017, at 17:24, Suraj Thyagaraj <[log in to unmask]> wrote:
>
> Saad,
>
> That seems to have fixed the error but the output folder only contains one output fdt_paths.nii.gz and the waytotal has only one number, both of which are similar to the output when running tractography without any condition. Am I missing something?
>
> {FSLDIR}/bin/probtrackx2 -x $SEEDFILENAME --targetmasks=$TARGETSLIST -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s {BEDPOSTX_FOLDER}/merged -m {BEDPOSTX_FOLDER}/nodif_brain_mask --dir=${OUTPUT_FOLDER} --otargetpaths
>
> Thanks,
> /Suraj
>
