Yes, you can use mri_binarize with the --surf output option

On 08/26/2018 08:22 PM, Russell Butler wrote:

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hello, i would like to create a mesh, such as the one in surf/lh.pial, using an arbitrary binary volume.

i'm aware that freesurfer can convert the subcortical volume ROIs to surfaces, does anyone know if this can be applied to an arbitrary binary volume?

i would like to replicate the script by Anderson Winkler (see below) but instead of on subcortical aseg, on an arbitrary volume that i supply. is this possible? thanks,

# Pre-tessellate     echo "==> Pre-tessellating: ${s}, ${lab0}"     ${FREESURFER_HOME}/bin/mri_pretess \            ${SUBJECTS_DIR}/${s}/mri/aseg.mgz ${lab} \            ${SUBJECTS_DIR}/${s}/mri/norm.mgz \  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz

# Tessellate     echo "==> Tessellating: ${s}, ${lab0}"     ${FREESURFER_HOME}/bin/mri_tessellate \  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_filled.mgz \            ${lab} ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth

# Smooth     echo "==> Smoothing: ${s}, ${lab0}"     ${FREESURFER_HOME}/bin/mris_smooth -nw \  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}_notsmooth \            ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}

# Convert to ASCII     echo "==> Converting to ASCII: ${s}, ${lab0}"     ${FREESURFER_HOME}/bin/mris_convert \            ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0} \  ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc     mv ${SUBJECTS_DIR}/${s}/tmp/${RNDSTR}/aseg_${lab0}.asc \        ${SUBJECTS_DIR}/${s}/ascii/aseg_${lab0}.srf

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