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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