*** empty log message ***

bedpost_datacheck

@@ -7,9 +7,9 @@ fi
 
 DIR=$1;
 for img in ${DIR}/data ${DIR}/nodif ${DIR}/nodif_brain_mask ;do
-    if [ `imtest $img` -eq 1 ] ; then
+    if [ `${FSLDIR}/bin/imtest $img` -eq 1 ] ; then
 	echo $img
-	avwinfo $img;
+	${FSLDIR}/bin/avwinfo $img;
 	echo ""
     else
 	echo $img does not exist;
@@ -18,30 +18,30 @@ done
 
 for bv in ${DIR}/bvals ${DIR}/bvecs;do
     echo " num lines in $bv "
-    cat $bv|wc -l |grep -v "^ *$"
+    cat $bv |grep -v "^ *$"|wc -l
     echo " num words in $bv "
     cat $bv|wc -w
 done
 
-if [ `imtest ${DIR}/data` -eq 1 -a `imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
+if [ `${FSLDIR}/bin/imtest ${DIR}/data` -eq 1 -a `${FSLDIR}/bin/imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
 
-    dx=`avwval ${DIR}/data dim1`
-    dy=`avwval ${DIR}/data dim2`
-    dz=`avwval ${DIR}/data dim3`
-    dt=`avwval ${DIR}/data dim4`
+    dx=`${FSLDIR}/bin/avwval ${DIR}/data dim1`
+    dy=`${FSLDIR}/bin/avwval ${DIR}/data dim2`
+    dz=`${FSLDIR}/bin/avwval ${DIR}/data dim3`
+    dt=`${FSLDIR}/bin/avwval ${DIR}/data dim4`
     
-    nbmx=`avwval ${DIR}/nodif_brain_mask dim1`
-    nbmy=`avwval ${DIR}/nodif_brain_mask dim2`
-    nbmz=`avwval ${DIR}/nodif_brain_mask dim3`
+    nbmx=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim1`
+    nbmy=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim2`
+    nbmz=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim3`
     
     
     if [ $dx -ne $nbmx -o  $dy -ne $nbmy -o $dz -ne $nbmz ];then 
 	echo "data dimensions do not match mask dimensions"
     fi
     
-    bvallen=`cat ${DIR}/bvals|wc -w|grep -v "^ *$"`
+    bvallen=`cat ${DIR}/bvals|grep -v "^ *$"|wc -w`
     bveclenw=`cat ${DIR}/bvecs|wc -w`
-    bveclenl=`cat ${DIR}/bvecs|wc -l|grep -v "^ *$"`
+    bveclenl=`cat ${DIR}/bvecs|grep -v "^ *$"|wc -l`
     bveclen=`echo "$bveclenw / $bveclenl"|bc`