External Email - Use Caution Hi Jan,
mri_vol2surf is not the correct command to achieve this. Use mri_mc or mri_tesselate. See also https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61335.html Antonin Skoch Dear Freesurfer experts, I would like to run tractography using probtrackx2 tool from one seed ROI (cortex) through another waypoint ROI. I need both these masks (ROIs) in gii format. Seed ROI I extracted using Freesurfer (recon-all, mri_convert and label2surf functions). Then I drew second waipoint ROI using FSLeyes edit tool, saved it as binary nii.gz file and tried to convert it to surface gii file using mri_vol2surf:mri_vol2surf --src mask.nii.gz --out mask.gii --regheader <SUB> --reg fsl2freesurfer.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, Jan
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