Hi
I am forwarding to the list.
You need an “=“ sign for the target mask option. In general, you need an equal sign whenever the option takes two “-“ instead of one.
The targets will be treated as waypoints, not stop masks.
Cheers
Saad
> On 16 May 2017, at 16:55, Suraj Thyagaraj <[log in to unmask]> wrote:
>
> Saad,
>
> Thanks for your response!
>
> I am fairly new to the platform and I'm not sure if I understand the proper usage with the targetmasks option as I'm getting en error message with this code:
>
> {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
>
> SEEDFILENAME points to a single NIFTI image
> TARGETSLIST points to a text file with all the targets that I'd like to use as individual waypoints
>
> Also, how do I specify to treat each of the target masks as waypoints (and not endpoints)?
>
> Regards,
> /Suraj
>
>
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