diff --git a/sienax b/sienax index e95e5e52ab5e45730bd3b3619e81d09bc24bca8b..1a7a022c91dd446f33dfc555ef972c450613c13e 100755 --- a/sienax +++ b/sienax @@ -150,10 +150,15 @@ if [ $nseg = 2 ] ; then xb=`echo $S | awk '{print $3}'` brain=`echo "2 k $xa $xb * $vscale * p" | dc -` else + if [ _$lm != _ ] ; then + ${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_talmaskbrain ${I}_talmaskbrain + fi + ${FSLDIR}/bin/fast $imtype -e -ov $@ ${I}_talmaskbrain >> ${I}.sienax 2>&1 if [ _$lm != _ ] ; then - ${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_talmaskbrain_pve_1 ${I}_talmaskbrain_pve_1 + ${FSLDIR}/bin/avwmaths_32R $lm -bin -max ${I}_talmaskbrain_pve_2 ${I}_talmaskbrain_pve_2 + ${FSLDIR}/bin/avwmaths_32SI $lm -bin -mul 3 -max ${I}_talmaskbrain_seg ${I}_talmaskbrain_seg fi echo "" >> ${I}.sienax