Added an option -m for saving the matrix directly to a file, and also used...

Added an option -m for saving the matrix directly to a file, and also used tmpnam to avoid clashing outputs for temporary *_nii.mat file

fslreorient2std

@@ -2,7 +2,7 @@
 
 #   reorientation script
 #
-#   Matthew Webster
+#   Matthew Webster and Mark Jenkinson
 #   FMRIB Image Analysis Group
 #
 #   Copyright (C) 2012 University of Oxford
@@ -10,7 +10,7 @@
 #   SHCOPYRIGHT
 
 if [ $# -lt 1 ] ; then 
-  echo "Usage: `basename $0` <input_image> [output_image]"
+  echo "Usage: `basename $0` [-m <matrix file>] <input_image> [output_image]"
   echo " "
   echo "`basename $0` is a tool for reorienting the image to match the"
   echo "approximate orientation of the standard template images (MNI152)."
@@ -21,12 +21,19 @@ if [ $# -lt 1 ] ; then
   echo "assumes the labels are correct - if not, fix that before using this."
   echo "If the output name is not specified the equivalent transformation"
   echo " matrix is written to the standard output"
+  echo "If the option -m is given, with an accompanying filename, then the"
+  echo " transformation matrix is written to this file instead"
   echo " "
   exit 1
 fi
 
+if [ $1 = -m ] ; then
+    matfn=$2
+    shift 2
+fi
 img=`$FSLDIR/bin/remove_ext $1`;
 outimg=$2;
+tmpfn=`$FSLDIR/bin/tmpnam`
 
 if [ `$FSLDIR/bin/imtest $img` = 0 ] ; then
   echo "ERROR: Could not find image $1" 1>&2
@@ -47,15 +54,23 @@ pattern=sto_xyz
 if [ $scode = 0 ] ; then
   pattern=qto_xyz
 fi
-$FSLDIR/bin/fslhd $img | grep $pattern | awk '{ print $2 " " $3 " " $4 " " $5  }' > ${outimg}_nii.mat
-det=`$FSLDIR/bin/avscale ${outimg}_nii.mat | grep Determinant | awk '{ print $3 }'`;
+$FSLDIR/bin/fslhd $img | grep $pattern | awk '{ print $2 " " $3 " " $4 " " $5  }' > ${tmpfn}_nii.mat
+det=`$FSLDIR/bin/avscale ${tmpfn}_nii.mat | grep Determinant | awk '{ print $3 }'`;
 if [ X`echo "if ( $det < 0 ) { 1 }" | bc -l` = X1 ] ; then
     # radiological case (negative determinant)
-    $FSLDIR/bin/fslswapdim $img RL PA IS $outimg
+    LeftRight=RL
+else
+    LeftRight=LR
+fi
+if [ X$matfn = X ] ; then
+    $FSLDIR/bin/fslswapdim $img $LeftRight PA IS $outimg
 else
-    $FSLDIR/bin/fslswapdim $img LR PA IS $outimg
+    $FSLDIR/bin/fslswapdim $img $LeftRight PA IS > $matfn
+    if [ X$outimg != X ] ; then
+	$FSLDIR/bin/fslswapdim $img $LeftRight PA IS $outimg
+    fi
 fi
 
 # clean up
-rm -f ${outimg}_nii.mat
+rm -f ${tmpfn}_nii.mat ${tmpfn}