You can use mri_surf2vol with the --mkmask option (method 2; see mri_surf2vol --help), eg,
cd subject/surf
mri_surf2vol --mkmask --hemi lh --o mask.lh.mgz --identity subject --template ../mri/nu.mgz
If you want to go to another volume, supply the registration to that volume with --reg instead of using --identity

On 12/16/2024 5:13 AM, Tamir Eisenstein wrote:

External Email - Use Caution

Dear FreeSurfer experts,

Is it possible using the FS tools to create a grey-white matter boundary binary mask in volume space (e.g., a nifti file) that will be a single voxel thick along the entire grey-white matter boundary?

Many thanks,

Tamir

Dr Tamir Eisenstein, Ph.D.

Postdoctoral Researcher

FMRIB, Wellcome Centre for Integrative Neuroimaging

Nuffield Department of Clinical Neurosciences

John Radcliffe Hospital, Oxford OX3 9DU

University of Oxford

tamir.eisenstein@ndcn.ox.ac.uk

eisentamir@gmail.com

tel: +44 7938790763
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