Hi Jan
Looks like the bit you are asking about is the output of a FreeSurfer command (mri_vol2surf) so probably best to ask on their forum - unless someone else on this forum can chime in?
Cheers
Saad
> On 17 Jun 2019, at 11:00, Jan Valošek <[log in to unmask]> wrote:
>
> Dear experts,
> I would like to run probtrackx2 with gii masks.So, I ran recon-all and extracted one selected cortical surface ROI using label2surf. I will use this ROI as seed mask. As waypoint mask I would like to use manually drawn mask. I drew this mask using FSLeyes edit tool, saved it as binary nii.gz file and converted to surface gii file using mri_vol2surf:
>
> mri_vol2surf --src mask.nii.gz --out mask.gii --regheader <SUB> --reg freesurfer2fsl.dat --sd <SUB>/surf --hemi rh --surf pial --projfrac-max 0 1 0.05 --out_type gii
>
> But, converted ROI looks empty. Do I have any mistake in command above or is there any another way how to convert nii -> gii?
>
> Thanks in advance,
> Jan
>
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