Hi
> On 5 Feb 2019, at 01:37, SUBSCRIBE FSL Erik <[log in to unmask]> wrote:
>
> Hi FSL team
> I am new to using surfaces as ROIs in probtrackx and could not find the answer to a few questions I had:
> 1. Can the generated .gii surface files be based directly to classification targets?
yes as long as the gifti surface file contains both the geometry (vertices and faces) as well as the roi (scalars on vertices)
> If so, is it possible to mix surface targets with a standard subcortical .nii seed volume, such as that generated from FIRST segmentation?
yes, just create a text file that lists both the surface and voxel file names (with full path) and they will be treated inside probtrackx2 as if they were a single roi.
>
> 2. I would like to modify the surfaces generated by the FreeSurfer atlas. For instance, if I wanted to subtract the BA6 label from the Superior Frontal label, is that possible? Is it valid to just subtract these genereated .gii surface files in fslmaths?
you can use surfmaths for that (works like fslmaths but with surface files). in this case you can just use the func.gii style file (ie without the geometry encoded in the file)
cheers
saad
>
> Thanks!
>
> Erik
>
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