Making the scripts more portable for FMRIB cayenne & jalapeno clusters

bedpost

@@ -5,7 +5,15 @@
 #   SHCOPYRIGHT
 
 if [ "x$SGE_ROOT" = "x" ] ; then
-  . /usr/local/share/sge-6.0/default/common/settings.sh
+  if [ -f /usr/local/share/sge-6.0/default/common/settings.sh ] ; then
+    . /usr/local/share/sge-6.0/default/common/settings.sh
+  else if [ -f /usr/local/sge-6/default/common/settings.sh ] ; then
+      . /usr/local/sge-6/default/common/settings.sh
+    else
+      echo "bedpost: Couldn\'t locate SGE_ROOT\!"
+      exit 255
+    fi
+  fi
 fi
 
 Usage() {

bedpostX

@@ -5,12 +5,20 @@
 #   SHCOPYRIGHT
 
 if [ "x$SGE_ROOT" = "x" ] ; then
-  . /usr/local/share/sge-6.0/default/common/settings.sh
+  if [ -f /usr/local/share/sge-6.0/default/common/settings.sh ] ; then
+    . /usr/local/share/sge-6.0/default/common/settings.sh
+  else if [ -f /usr/local/sge-6/default/common/settings.sh ] ; then
+      . /usr/local/sge-6/default/common/settings.sh
+    else
+      echo "bedpost: Couldn\'t locate SGE_ROOT\!"
+      exit 255
+    fi
+  fi
 fi
 
 Usage() {
     echo ""
-    echo "Usage: bedpost <subject directory> "
+    echo "Usage: bedpostX <subject directory> "
     echo ""
     echo "expects to find bvals and bvecs in subject directory"
     echo "expects to find data nodif_brain_mask nodif in subject directory"

bedpostX_single_slice.sh

@@ -7,7 +7,6 @@ slicezp=`${FSLDIR}/bin/zeropad $slice 4`
 #$ -cwd -q long.q
 #$ -S /bin/sh
 #$ -V -N bedpostX
-#$ -l arch=tru64
 #$ -m a
 
 ${FSLDIR}/bin/xfibres\

bedpost_single_slice.sh

@@ -7,7 +7,6 @@ slicezp=`${FSLDIR}/bin/zeropad $slice 4`
 #$ -cwd -q long.q
 #$ -S /bin/sh
 #$ -V -N bedpost
-#$ -l arch=tru64
 #$ -m a
 
 ${FSLDIR}/bin/diff_pvm\