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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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