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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