From 80acccf9292a3affd41355ee063d3e902f48857e Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Mon, 13 Aug 2012 10:44:06 +0000
Subject: [PATCH] Changes to avoid unnecessary processing
---
fslreorient2std | 18 ++++++++++++++----
fslswapdim | 33 ++++++++++++++++++++++++++-------
fslswapdim.cc | 14 +++++++++++++-
3 files changed, 53 insertions(+), 12 deletions(-)
diff --git a/fslreorient2std b/fslreorient2std
index f8453a3..2bcffd2 100755
--- a/fslreorient2std
+++ b/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
+
diff --git a/fslswapdim b/fslswapdim
index 4333a70..4b173f0 100755
--- a/fslswapdim
+++ b/fslswapdim
@@ -1,4 +1,5 @@
#!/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
diff --git a/fslswapdim.cc b/fslswapdim.cc
index 7601d54..8b504a0 100644
--- a/fslswapdim.cc
+++ b/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;
}
--
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