*** empty log message ***

siena

@@ -101,6 +101,8 @@ sdo="${sdo}${is_t2}"
 echo "----------  extract brain  --------------------------------------------" >> ${A}_to_${B}.siena
 ${FSLDIR}/bin/bet $A ${A}_brain -s -m $betopts >> ${A}_to_${B}.siena
 ${FSLDIR}/bin/bet $B ${B}_brain -s -m $betopts >> ${A}_to_${B}.siena
+${FSLDIR}/bin/avwmaths++ ${A}_brain -sub `$FSLDIR/bin/avwstats++ ${A}_brain -p 0` -mas ${A}_brain_mask ${A}_brain -odt float
+${FSLDIR}/bin/avwmaths++ ${B}_brain -sub `$FSLDIR/bin/avwstats++ ${B}_brain -p 0` -mas ${B}_brain_mask ${B}_brain -odt float
 
 echo ""                                                                        >> ${A}_to_${B}.siena
 echo "----------  register brains and skulls  -------------------------------" >> ${A}_to_${B}.siena

sienax

@@ -101,7 +101,8 @@ if [ $regional = 1 ] ; then
 fi
 
 echo "----------  extract brain  --------------------------------------------" >> ${I}.sienax
-${FSLDIR}/bin/bet $I ${I}_brain -s $betopts >> ${I}.sienax
+${FSLDIR}/bin/bet $I ${I}_brain -s -m $betopts >> ${I}.sienax
+${FSLDIR}/bin/avwmaths++ ${I}_brain -sub `$FSLDIR/bin/avwstats++ ${I}_brain -p 0` -mas ${I}_brain_mask ${I}_brain -odt float
 
 echo ""                                                                        >> ${I}.sienax
 echo "----------  register to stdairach space using brain and skull  --------" >> ${I}.sienax