Hi Freesurfer experts,

I am trying to perform whole brain tractography using FSL's Probtrackx2 with Freesurfer white surfaces as seed and pial surfaces as targets. To obtain a whole brain connectivity graph I need the streamlines between the hemispheres. This means that I need to remove the part of the medial wall between the hemispheres corresponding to corpus callosum and anterior and posterior commissures.

One possible solution might be to use mri_surf2vol to transform the white surfaces to volumes and hereafter multiply by corpus callosum and anterior and posterior commissures to cut holes in the white surface. After removing the relevant parts the volume is transformed back to a surface which is used as input to the tractography. I don't know if this is the best way to do it or if there is a better way to automatically obtain the whole brain white/pial surface?

Any thoughts and comments are highly appreciated.

Best, Karen