new tests for FSL5 versions of fslswapdim and fslreorient2std

tests/fslswapdim_test.sh

@@ -2,26 +2,39 @@
 
 ## NOTE: needs links or copies of various fsl utilities to exist in ../bin at the moment (annoyingly!)
 
-num=1;
-for aa in RL LR ; do
-    for bb in RL LR ; do
-	for cc in RL LR ; do
-	    for tr1 in RLAPSI RLSIAP APSIRL APRLSI SIRLAP SIAPRL ; do
-		aaa=`echo $aa | tr R ${tr1:0:1} | tr L ${tr1:1:1}`;
-		bbb=`echo $bb | tr R ${tr1:2:1} | tr L ${tr1:3:1}`;
-		ccc=`echo $cc | tr R ${tr1:4:1} | tr L ${tr1:5:1}`;
-		echo $aaa $bbb $ccc
-		( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslswapdim /usr/local/fsl/data/standard/MNI152_T1_2mm $aaa $bbb $ccc fooNEW_$num )
-		echo $FSLDIR
-		$FSLDIR/bin/fslswapdim $FSLDIR/data/standard/MNI152_T1_2mm $aaa $bbb $ccc fooOLD_$num
-		diff fooNEW_${num}.nii.gz fooOLD_${num}.nii.gz
-		num=`echo $num + 1 | bc`
-	    done
-	done
-    done
+mni=/home/fs0/mark/fslsrc/avwutils/tests/mni
+#mni=$FSLDIR/data/standard/MNI152_T1_2mm
+
+
+for fn in fooOLD_*.nii.gz ; do
+    echo $fn
+    ( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslreorient2std $mni  fooRNEW )
+    ( export FSLDIR=/usr/local/fsl-alpha ; $FSLDIR/bin/fslreorient2std $mni fooROLD )
+    diff fooRNEW.nii.gz fooROLD.nii.gz
 done
 
 
+
+# num=1;
+# for aa in RL LR ; do
+#     for bb in RL LR ; do
+# 	for cc in RL LR ; do
+# 	    for tr1 in RLAPSI RLSIAP APSIRL APRLSI SIRLAP SIAPRL ; do
+# 		aaa=`echo $aa | tr R ${tr1:0:1} | tr L ${tr1:1:1}`;
+# 		bbb=`echo $bb | tr R ${tr1:2:1} | tr L ${tr1:3:1}`;
+# 		ccc=`echo $cc | tr R ${tr1:4:1} | tr L ${tr1:5:1}`;
+# 		echo $aaa $bbb $ccc
+# 		( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooNEW_$num )
+# 		echo $FSLDIR
+# 		( export FSLDIR=/usr/local/fsl-alpha ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooOLD_$num )
+# 		diff fooNEW_${num}.nii.gz fooOLD_${num}.nii.gz
+# 		num=`echo $num + 1 | bc`
+# 	    done
+# 	done
+#     done
+# done
+
+
 # num=1;
 # for aa in x -x ; do
 #     for bb in x -x ; do
@@ -31,9 +44,9 @@ done
 # 		bbb=`echo $bb | tr x ${tr1:1:1}`;
 # 		ccc=`echo $cc | tr x ${tr1:2:1}`;
 # 		echo $aaa $bbb $ccc
-# 		( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslswapdim /usr/local/fsl/data/standard/MNI152_T1_2mm $aaa $bbb $ccc fooNEW_$num )
+# 		( export FSLDIR=`pwd`/.. ; $FSLDIR/bin/fslswapdim $mni  $aaa $bbb $ccc fooNEW_$num )
 # 		echo $FSLDIR
-# 		$FSLDIR/bin/fslswapdim $FSLDIR/data/standard/MNI152_T1_2mm $aaa $bbb $ccc fooOLD_$num
+# 		( export FSLDIR=/usr/local/fsl-alpha ; $FSLDIR/bin/fslswapdim $mni $aaa $bbb $ccc fooOLD_$num )
 # 		diff fooNEW_${num}.nii.gz fooOLD_${num}.nii.gz
 # 		num=`echo $num + 1 | bc`
 # 	    done