diff --git a/recon_surf/recon-surf.sh b/recon_surf/recon-surf.sh index 21619522..82baddee 100755 --- a/recon_surf/recon-surf.sh +++ b/recon_surf/recon-surf.sh @@ -884,6 +884,11 @@ else echo "pushd $mdir" >> $CMDF # these are run automatically in fs7* recon-all and cannot be called directly without -pial flag (or other t2 flags) + if [ "$fssurfreg" == "1" ] ; then + # jacobian needs sphere reg which might be turned off by user (on by default) + cmd="mris_jacobian ../surf/$hemi.white ../surf/$hemi.sphere.reg ../surf/$hemi.jacobian_white" + RunIt "$cmd" $LF $CMDF + fi cmd="mris_place_surface --curv-map ../surf/$hemi.white 2 10 ../surf/$hemi.curv" RunIt "$cmd" $LF $CMDF cmd="mris_place_surface --area-map ../surf/$hemi.white ../surf/$hemi.area"