Andrew Janke patch

bedpostx

@@ -135,9 +135,12 @@ EOM
     ${subjdir}.bedpostX/monitor&
     monitorpid=$!
 fi
-for ((slice=0; slice < $nslices; slice++)) ; do
+slice=0
+while [ $slice -le $nslices ]
+do
     echo "${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $njumps $sampleevery $slice" \
 	>> ${subjdir}.bedpostX/commands.txt
+    slice=$(($slice + 1))
 done
 bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
 [ "x$SGE_ROOT" = "x" ] && kill $monitorpid

bedpostx_postproc.sh

@@ -11,7 +11,9 @@ subjdir=$1
 
 numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples | wc -w | awk '{print $1}'`
 
-for ((fib=1; fib<=$numfib; fib++));do
+fib=1
+while [ $fib -le $numfib ]
+do
     ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
     ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
     ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples  `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
@@ -20,6 +22,7 @@ for ((fib=1; fib<=$numfib; fib++));do
     ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${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=$(($fib + 1))
 done
 
 echo Removing intermediate files