Yes, you can use mri_binarize with the --surf output option
On 08/26/2018 08:22 PM, Russell Butler wrote:
>
> External Email - Use Caution
>
> 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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