*** empty log message ***

siena_flow2std

@@ -42,7 +42,7 @@ if [ ! -f ${A}_to_std.mat ] ; then
     if [ `${FSLDIR}/bin/imtest ${A}_brain` = 0 ] ; then
 	${FSLDIR}/bin/bet $A ${A}_brain
     fi
-    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_std.mat
+    ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_std.mat -o ${A}_to_std
 fi
 ${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_inv.mat -inverse ${A}_halfwayto_${B}.mat
 ${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_to_std.mat -concat ${A}_to_std.mat ${A}_halfwayto_${B}_inv.mat
@@ -59,6 +59,6 @@ ${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg1
 
 # cleanup
 if [ $debug = 0 ] ; then
-    /bin/rm -f ${A}_halfwayto_${B}_inv.mat `$FSLDIR/bin/imglob ${A}_brain.* ${A}_to_${B}_flow_dil.*`
+    /bin/rm -f ${A}_halfwayto_${B}_inv.mat `$FSLDIR/bin/imglob -oneperimage ${A}_brain.* ${A}_to_${B}_flow_dil.* ${A}_to_std.*`
 fi