diff --git a/bedpostx b/bedpostx index 04b7498a77086fda578101c2c6fc8e0f3bb755ba..08295a8f897b1296abc41e9b5d85b216f1b1b288 100755 --- a/bedpostx +++ b/bedpostx @@ -24,6 +24,7 @@ Usage() { echo "-b (burnin period, default 1000)" echo "-j (number of jumps, default 1250)" echo "-s (sample every, default 25)" + echo "-model (1:monoexponential [default] - 2:non-monoexponential [to be used in multi-shell acquisitions])" echo "" exit 1 } @@ -54,6 +55,7 @@ fudge=1 burnin=1000 njumps=1250 sampleevery=25 +model=1 while [ ! -z "$2" ] do case "$2" in @@ -62,6 +64,7 @@ do -b) burnin=$3;shift;; -j) njumps=$3;shift;; -s) sampleevery=$3;shift;; + -model) model=$3;shift;; *) break;; esac shift @@ -173,12 +176,12 @@ do if [ `$FSLDIR/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ];then echo "slice $slice has already been processed" else - echo "${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $njumps $sampleevery $slice" \ + echo "${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $njumps $sampleevery $model $slice" \ >> ${subjdir}.bedpostX/commands.txt fi slice=$(($slice + 1)) done -bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt` +bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -a lx24-amd64 -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt` echo Queuing post processing stage mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir` diff --git a/bedpostx_postproc.sh b/bedpostx_postproc.sh index 6cee95b4c742a99507ff63428ac00377e64c95d2..4115d2c24c9c54dfa46b4b05aab9c2829e1999c5 100755 --- a/bedpostx_postproc.sh +++ b/bedpostx_postproc.sh @@ -16,8 +16,17 @@ do ${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 + +if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_dsamples` ];then + ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_dsamples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_dsamples*` +fi +if [ `${FSLDIR}/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_0000/mean_d_stdsamples` ];then + ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/mean_d_stdsamples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/mean_d_stdsamples*` +fi + echo Removing intermediate files if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then