If not is set SGE_ROOT don't use any queue. Improve monitor if not SGE

CUDA/bedpostx_gpu

@@ -64,7 +64,7 @@ subjdir=`echo $subjdir | sed 's/\/$/$/g'`
 echo subjectdir is $subjdir
 
 #parse option arguments
-queue=cuda.q
+queue="-q cuda.q"
 njobs=1
 nfibres=2
 fudge=1
@@ -73,12 +73,15 @@ njumps=1250
 sampleevery=25
 model=1
 gflag=0
+if [ "x$SGE_ROOT" = "x" ]; then
+	queue=''
+fi
 
 shift
 while [ ! -z "$1" ]
 do
   case "$1" in
-      -Q) queue=$2;shift;;
+      -Q) queue=-q $2;shift;;
       -NJOBS) njobs=$2;shift;;
       -n) nfibres=$2;shift;;
       -w) fudge=$2;shift;;
@@ -147,6 +150,8 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
     ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
 fi
 
+nvox=`${FSLDIR}/bin/fslstats $subjdir.bedpostX/nodif_brain_mask -V  | cut -d ' ' -f1 `
+
 echo Queuing parallel processing stage
 [ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
 if [ "x$SGE_ROOT" = "x" ]; then
@@ -158,24 +163,33 @@ if [ "x$SGE_ROOT" = "x" ]; then
 #!/bin/sh
 finished=0
 logdir=${subjdir}.bedpostX/logs
+#voxels processed in each subpart are 12800 or more if the last one is less than 6400 (1 part less)
+nsubparts=\$(($nvox/12800))
+if [ \$nsubparts%12800 != 0 ];then 
+	nsubparts=\$((\$nsubparts + 1)) 
+fi
+last_part=\$(($nvox-(((\$nsubparts-1))*12800)))
+if [ \$last_part -lt 6400 ];then 
+	nsubparts=\$((\$nsubparts - 1)) 
+fi
 
 check() {
     if [ \$finished -eq 1 ];then
-        echo "\$nfin parts processed of "$njobs
+        echo "\$nfin parts processed of "$nsubparts
     else
         nfin=0
-        part=0
-        while [ "\$part" -le $njobs ];do
+        subpart=0
+         while [ "\$subpart" -le \$nsubparts ];do
             partzp=\`\$FSLDIR/bin/zeropad \$part 4\`
-            if [ -f ${subjdir}.bedpostX/diff_parts/data_part_\$partzp/mean_S0samplesJ ];then
+            if [ -f ${subjdir}.bedpostX/diff_parts/data_part_0000/mean_S0samples_\$subpart ];then
                 nfin=\$((\$nfin + 1))
             fi
-                part=\$((\$part + 1))
+                subpart=\$((\$subpart + 1))
         done
-        if [ \$nfin -eq $njobs ] ; then
+        if [ \$nfin -eq \$nsubparts ] ; then
             finished=1
         fi
-        echo "\$nfin parts processed of "$njobs
+        echo "\$nfin parts processed of "\$nsubparts
     fi
 }
 exit_test() {
@@ -193,7 +207,7 @@ check
 n=0
 while [ \$finished -eq 0 ] ; do
     sleep 10
-    if [ \$n -eq 60 ] ; then
+    if [ \$n -eq 6 ] ; then
         check
         n=0
     else
@@ -221,11 +235,10 @@ do
     	part=$(($part + 1))
 done
 
-bedpostid=`${FSLDIR}/bin/fsl_sub -q $queue -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx_gpu -t ${subjdir}.bedpostX/commands.txt`
+bedpostid=`${FSLDIR}/bin/fsl_sub $queue -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx_gpu -t ${subjdir}.bedpostX/commands.txt`
 
 echo Queuing post processing stage
-nvox=`${FSLDIR}/bin/fslstats $subjdir.bedpostX/nodif_brain_mask -V   | cut -d ' ' -f1 `
-mergeid=`${FSLDIR}/bin/fsl_sub -q $queue -j $bedpostid -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDEVDIR}/bin/bedpostx_postproc_gpu.sh --data=${subjdir}/data --mask=$subjdir.bedpostX/nodif_brain_mask -b ${subjdir}.bedpostX/bvals -r ${subjdir}.bedpostX/bvecs  --forcedir --logdir=$subjdir.bedpostX/diff_parts $gopts $nvox $njobs ${subjdir}`
+mergeid=`${FSLDIR}/bin/fsl_sub $queue -j $bedpostid -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDEVDIR}/bin/bedpostx_postproc_gpu.sh --data=${subjdir}/data --mask=$subjdir.bedpostX/nodif_brain_mask -b ${subjdir}.bedpostX/bvals -r ${subjdir}.bedpostX/bvecs  --forcedir --logdir=$subjdir.bedpostX/diff_parts $gopts $nvox $njobs ${subjdir}`
 
 [ "x$SGE_ROOT" = "x" ] && kill -USR1 $monitorpid
 if [ "x$SGE_ROOT" != "x" ]; then