Hi Leonardo
The different ROIs are actually treated as a single ROI if you use them all inside a single NIFTI volume (probtrackx2 does not assume they have labels). If you want them treated as separate ROIs, you can pass a list of separate NIFTI files (one per ROI) in a single text file.
Cheers
Saad
> On 26 Nov 2019, at 14:30, Leonardo Cerliani <[log in to unmask]> wrote:
>
> Hello everybody!
>
> I am trying to carry out a probtrackx2 with omatrix3 option. Everything goes well, however the third column of the resulting coords_for_fdt_matrix3, which should contain the indices of the ROIs in my seed mask (nifti volume with different integers indexing different ROIs), is all zeros.
>
> This prevents me to aggregate voxelwise connection probability counts across ROIs using Saad's instructions here:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;5f3e10d9.1401
>
> Can you please help?
> Thanks a lot in advance!
>
> all the best,
> leonardo
>
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