Changes to avoid unnecessary processing

fslreorient2std

@@ -24,8 +24,8 @@ if [ `$FSLDIR/bin/imtest $img` = 0 ] ; then
   exit 2
 fi
 
-scode=`$FSLDIR/bin/fslorient -getsformcode $img`;
-qcode=`$FSLDIR/bin/fslorient -getqformcode $img`;
+scode=`$FSLDIR/bin/fslval $img sform_code`;
+qcode=`$FSLDIR/bin/fslval $img qform_code`;
 if [ $scode = 0 -a $qcode = 0 ] ; then
   echo "ERROR: Orientation information not stored in ${1}!"
   echo "Cannot reslice without orientation information (i.e. need valid labels in FSLView)"
@@ -34,9 +34,19 @@ if [ $scode = 0 -a $qcode = 0 ] ; then
   exit 3
 fi
 
-hand=`$FSLDIR/bin/fslorient -getorient $img`;
-if [ $hand = RADIOLOGICAL ] ; then
+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 }'`;
+if [ X`echo "if ( $det < 0 ) { 1 }" | bc -l` = X1 ] ; then
+    # radiological case (negative determinant)
     $FSLDIR/bin/fslswapdim $img RL PA IS $outimg
 else
     $FSLDIR/bin/fslswapdim $img LR PA IS $outimg
 fi
+
+# clean up
+rm -f ${outimg}_nii.mat
+

fslswapdim

 #!/bin/sh
+set -e
 
 #   Extended syntax for fslswapdim
 #
@@ -27,7 +28,6 @@ get_axis(){
     echo $ax;
 }
 
-
 if [ $# -lt 4 ] ; then
   echo "Usage: fslswapdim <input> <a> <b> <c> [output]
 
@@ -41,6 +41,7 @@ if [ $# -lt 4 ] ; then
   exit 1;
 fi
 
+
 filetype=`$FSLDIR/bin/fslval $1 file_type`;
 if [ $filetype = "ANALYZE-7.5" ] ; then
     nifti=no;
@@ -62,7 +63,9 @@ fi
 
 uselabels=no
 
-comm="$FSLDIR/bin/fslswapdim_exe $1"
+comm1="$FSLDIR/bin/fslswapdim_exe $1"
+comm2=""
+swaplabs=""
 for fn in $2 $3 $4 ; do
     cc=`echo Q$fn | sed 's/[RLAPIS]//g'`;
     if [ $cc = "Q" ] ; then
@@ -79,14 +82,30 @@ for fn in $2 $3 $4 ; do
     else 
 	cc=$fn;
     fi
-    comm="$comm $cc";
+    comm2="$comm2 $cc";
+    swaplabs="$swaplabs $cc"
 done
 
+# check if just a simple copy is good enough (only if an output filename is specified)
+if [ "$swaplabs" = " x y z" ] ; then
+    if [ X$5 != X ] ; then
+	if [ `$FSLDIR/bin/remove_ext $1` != `$FSLDIR/bin/remove_ext $5` ] ; then
+	    comm="$FSLDIR/bin/imcp $1 $5"
+	    $comm
+	    exit 0
+	fi
+    else
+	cat $FSLDIR/etc/flirtsch/ident.mat
+	exit 0
+    fi
+fi
+
+
 # Check if the labels are used *and* it is doing a left-right inversion
 if [ $uselabels = yes ] ; then
-    tmpf=`$FSLDIR/bin/tmpnam`_sd
-    $comm > $tmpf 2>&1
-    wl=`grep WARNING $tmpf | wc -l`;
+    # the line below just checks the swapping syntax - it does not require the true image, as any will do since the arguments are now reduced to x/y/z format
+    check="`$FSLDIR/bin/fslswapdim_exe $FSLDIR/data/standard/MNI152_T1_2mm_brain $comm2 --checkLR`"
+    wl=`echo $check | grep -i changed | wc -l`;
     if [ $wl -gt 0 ] ; then
 	echo "Cannot perform requested swap (NEUROLOGICAL/RADIOLOGICAL storage inverted)"
 	echo "Try the following command instead:"
@@ -96,7 +115,7 @@ if [ $uselabels = yes ] ; then
     fi
 fi
 
-comm="$comm $5"
+comm="$comm1 $comm2 $5"
 
 # verbose?
 #echo $comm

fslswapdim.cc

@@ -13,10 +13,11 @@
 using namespace NEWIMAGE;
 
 void print_usage(const string& progname) {
-  cout << "Usage: " << progname << " <input> <a> <b> <c> [output]" << endl;
+  cout << "Usage: " << progname << " <input> <a> <b> <c> [output] [--checkLR]" << endl;
   cout << endl;
   cout << "  where a,b,c represent the new x,y,z axes in terms of the" << endl;
   cout << "  old axes.  They can take values of -x,x,y,-y,z,-z" << endl;
+  cout << "  --checkLR  is an option that checks if the specified arguments lead to a Left-Right swap or not - it cannot be used with an output name" << endl;
   cout << "  e.g.  " << progname << " invol y x -z outvol" << endl;
 }
 
@@ -28,8 +29,13 @@ int fmrib_main(int argc,char *argv[])
   string inname=argv[1];
   string outname="";
   bool showmat=false;
+  bool checkonly=false;
   if (argc==6) {
     outname=argv[5];
+    if (outname=="--checkLR") {
+      outname="";
+      checkonly=true;
+    }
     showmat=false;
   } else {
     showmat=true;
@@ -45,6 +51,12 @@ int fmrib_main(int argc,char *argv[])
     cout << affmat << endl;
   }
 
+  if (checkonly) {
+    if (affmat.Determinant()<0.0) cout << "LR orientation changed" << endl;
+    else cout << "LR orientation preserved" << endl;
+    return 0;
+  } 
+
   if (affmat.Determinant()<0.0) {
     cout << "WARNING:: Flipping Left/Right orientation (as det < 0)" << endl;
   }