Hi Taha,
just to double check: did you have a look at the fdt_paths? Does that contain non-zero voxels? And is the number contained in the waytotal file bigger than 0?
I am just trying to make sure whether there were effectively were any streamlines that reached any of your target masks.
Cheers,
Matteo
> On 14 Sep 2017, at 04:30, Taha Abdullah <[log in to unmask]> wrote:
>
> Hello All,
>
> I am running probtrackx2 with a single seed and two classification targets in diffusion space. I am running on a single subject, I would eventually like to use the find_the_biggest to perform a hard segmentation on the seed. After browsing the listserv for solutions I could not find one, I was expecting three nifti files (fdt_paths and the seed_to_{targets}), however, there is only the fdt_paths. I found this recommendation below regarding a single seed and single target using the --otargetpaths (maybe it is deprecated?), but it still does not generate the two seed_to_target volumes. Can anyone advise? To be noted, the target masks are small.
>
> From 22 Jan 2016, at 04:07
> "If you have a single target mask, then you can get the relevant tract by also setting the target mask as a waypoint mask, and adding the —onewaycondition option.
>
> If you have multiple target masks, then you can use the (hidden) option: —otargetpaths. This will do the above but for each target separately, and output one file per target mask."
>
> Below is the logfile outputted from the GUI without the --otargetpaths:
>
> /usr/share/fsl/5.0/bin/probtrackx2 -x /home/share/freesurfer/subjects/$subject/mri/probtrackx_ROIs/lh/lh.seed2diff.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /home/share/freesurfer/subjects/$subject/diff_final/$subject/dmri.bedpostX/merged -m /home/share/freesurfer/subjects/$subject/diff_final/$subject/dmri.bedpostX/nodif_brain_mask --dir=/home/share/freesurfer/subjects/$subject/mri/probtrackx_ROIs/lh/output --waycond=AND --targetmasks=/home/share/freesurfer/subjects/$subject/mri/probtrackx_ROIs/lh/output/targets.txt --os2t
>
> I appreciate any insight
>
> Thank you,
> Taha
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