*** empty log message ***

bedpostx

@@ -73,45 +73,45 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
 	echo "${subjdir}/nodif_brain_mask not found"
 fi
 
-echo Making bedpost directory structure
+echo Making bedpostX directory structure
 
-mkdir -p ${subjdir}.bedpost/
-mkdir -p ${subjdir}.bedpost/diff_slices
-mkdir -p ${subjdir}.bedpost/logs
-mkdir -p ${subjdir}.bedpost/logs/pid_${$}
-mkdir -p ${subjdir}.bedpost/xfms
+mkdir -p ${subjdir}.bedpostX/
+mkdir -p ${subjdir}.bedpostX/diff_slices
+mkdir -p ${subjdir}.bedpostX/logs
+mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
+mkdir -p ${subjdir}.bedpostX/xfms
 
 mailto=`whoami`@fmrib.ox.ac.uk
 
 echo Queuing preprocessing stages
 preprocid=`qsub -M $mailto -V -q short.q \
-    -o ${subjdir}.bedpost/logs -e ${subjdir}.bedpost/logs \
+    -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs \
     ${FSLDIR}/bin/sge_bedpostX_preproc.sh ${subjdir} | \
     awk '{print $3}'`
 
 echo Queuing parallel processing stage
 nslices=`avwval ${subjdir}/data dim3`
 bedpostid=`qsub -M $mailto -hold_jid $preprocid -V -q long.q -t 1-$nslices \
-    -o ${subjdir}.bedpost/logs -e ${subjdir}.bedpost/logs \
+    -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs \
     ${FSLDIR}/bin/sge_bedpostX_single_slice.sh $subjdir | \
     awk '{print $3}' | awk -F. '{print $1}'`
 
 echo Queuing post processing stage
 mergeid=`qsub -M $mailto -hold_jid $bedpostid -V -q short.q \
-    -o ${subjdir}.bedpost/logs -e ${subjdir}.bedpost/logs \
+    -o ${subjdir}.bedpostX/logs -e ${subjdir}.bedpostX/logs \
     ${FSLDIR}/bin/sge_bedpostX_postproc.sh $subjdir | \
     awk '{print $3}'`
 
 echo
-echo Type ${subjdir}.bedpost/monitor to show progress.
-cat <<EOM > ${subjdir}.bedpost/monitor
+echo Type ${subjdir}.bedpostX/monitor to show progress.
+cat <<EOM > ${subjdir}.bedpostX/monitor
 #!/bin/sh
 finished=0
-logdir=${subjdir}.bedpost/logs
+logdir=${subjdir}.bedpostX/logs
 while [ \$finished -eq 0 ] ; do
     nfin=0
     if [ -f \$logdir/bedpost.o$bedpostid.1 ] ; then
-      nfin=\`cat \$logdir/bedpost.o$bedpostid.* |\
+      nfin=\`cat \$logdir/bedpostX.o$bedpostid.* |\
         grep Done | wc -w | awk '{print \$1}'\` 
     fi
     if [ \$nfin -eq $nslices ] ; then
@@ -122,14 +122,14 @@ while [ \$finished -eq 0 ] ; do
     sleep 600;
 done
 EOM
-chmod +x ${subjdir}.bedpost/monitor
+chmod +x ${subjdir}.bedpostX/monitor
 
-echo Type ${subjdir}.bedpost/cancel to terminate the task.
-cat <<EOC > ${subjdir}.bedpost/cancel
+echo Type ${subjdir}.bedpostX/cancel to terminate the task.
+cat <<EOC > ${subjdir}.bedpostX/cancel
 #!/bin/sh
 qdel $mergeid $bedpostid $preprocid
 EOC
-chmod +x ${subjdir}.bedpost/cancel
+chmod +x ${subjdir}.bedpostX/cancel
 
 echo
 echo You will get an email at the end of the post-processing stage.

bedpostx_postproc.sh

@@ -8,4 +8,41 @@ subjdir=$1
 #$ -m ae
 
 
-echo cock
\ No newline at end of file
+numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples |wc -w`
+
+
+fib=1;
+while [ $fib -le $numfib ];do
+    ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
+    ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
+    ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_f${fib}samples  `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
+    ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
+    ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
+    ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
+
+    ${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
+
+    fib=`echo "$fib +1"|bc`;
+done
+
+echo Removing intermediate files
+
+if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
+  if [ `imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
+    if [ `imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
+      rm -rf ${subjdir}.bedpostX/diff_slices
+      rm -f ${subjdir}/data_slice_*
+      rm -f ${subjdir}/nodif_brain_mask_slice_*
+    fi
+  fi
+fi
+
+echo Creating identity xfm
+
+xfmdir=${subjdir}.bedpostX/xfms
+echo 1 0 0 0 > ${xfmdir}/eye.mat
+echo 0 1 0 0 >> ${xfmdir}/eye.mat
+echo 0 0 1 0 >> ${xfmdir}/eye.mat
+echo 0 0 0 1 >> ${xfmdir}/eye.mat
+
+echo Done

bedpostx_preproc.sh

@@ -8,13 +8,13 @@ subjdir=$1
 #$ -m a
 
 echo Copying files to bedpost directory
-cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpost
-${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpost
+cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
+${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
 ${FSLDIR}/bin/avwmaths\
  ${subjdir}/nodif\
  -mas ${subjdir}/nodif_brain_mask\
- ${subjdir}.bedpost/nodif_brain
+ ${subjdir}.bedpostX/nodif_brain
 
 ${FSLDIR}/bin/avwslice ${subjdir}/data
 ${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
-echo Done
\ No newline at end of file
+echo Done

bedpostx_single_slice.sh

@@ -13,6 +13,6 @@ ${FSLDIR}/bin/xfibres\
  --data=$subjdir/data_slice_$slicezp\
  --mask=$subjdir/nodif_brain_mask_slice_$slicezp\
  -b $subjdir/bvals -r $subjdir/bvecs\
- --forcedir --logdir=$subjdir.bedpost/diff_slices/data_slice_$slicezp\
- --nj=1000 --bi=600 --se=20 --upe=24 --nfibres=2 > $subjdir.bedpost/logs/log$slicezp  && echo Done
+ --forcedir --logdir=$subjdir.bedpostX/diff_slices/data_slice_$slicezp\
+ --nj=1000 --bi=600 --se=20 --upe=24 --nfibres=2 > $subjdir.bedpostX/logs/log$slicezp  && echo Done