From 3ac99389b81b6882b066d7761aac6aeda9022509 Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Thu, 26 Aug 2004 16:22:38 +0000
Subject: [PATCH] *** empty log message ***
---
Makefile | 2 +-
diff_pvm.cc | 21 ++++++++++++---------
old_bedpost | 17 ++++++++---------
old_bedpost_proc | 6 +++---
4 files changed, 24 insertions(+), 22 deletions(-)
diff --git a/Makefile b/Makefile
index d9805c5..700463d 100644
--- a/Makefile
+++ b/Makefile
@@ -31,7 +31,7 @@ DIFF_PVMOBJS=diff_pvm.o diff_pvmoptions.o
RVOBJS=replacevols.o
MDVOBJS=make_dyadic_vectors.o
-SCRIPTS = eddy_correct bedpost bedpost_proc bedpost_clean_up bedpost_kill_all bedpost_kill_pid
+SCRIPTS = eddy_correct bedpost bedpost_proc bedpost_clean_up bedpost_kill_all bedpost_kill_pid zeropad
XFILES = dtifit probtrack find_the_biggest medianfilter diff_pvm make_dyadic_vectors
RUNTCLS = Fdt
diff --git a/diff_pvm.cc b/diff_pvm.cc
index 40c486f..6370a02 100644
--- a/diff_pvm.cc
+++ b/diff_pvm.cc
@@ -202,15 +202,15 @@ void Diff_pvmModel::setparams()
clear_params();
SinPrior thtmp(1);
- add_param("th",0.2,0.02,thtmp,true);
+ add_param("th",0.2,0.02,thtmp,true,true); //Will unwrap th param before saving
UnifPrior phtmp(0.2,2000*M_PI);
- add_param("ph",0, 0.02,phtmp,true);
+ add_param("ph",0, 0.02,phtmp,true,true); //Will unwrap th param before saving
UnifPrior ftmp(0,1);
- add_param("f",0.5,0.02,ftmp,true);
+ add_param("f",0.5,0.02,ftmp,true,true);
GammaPrior dtmp(4,1.0/0.0003); //test this out,
- add_param("d",0.005,0.00005,dtmp,true);
+ add_param("d",0.005,0.00005,dtmp,true,true);
UnifPrior S0tmp(0,100000);
- add_param("S0",10000,100,S0tmp,true);//false);
+ add_param("S0",10000,100,S0tmp,true,true);//false);
}
@@ -359,18 +359,21 @@ int main(int argc, char *argv[])
cout << "ntpts=" << ntpts << endl;
cout << "nvoxels=" << mask.getVolumeSize() << endl;
-
+
Diff_pvmModel model(bvecs,bvals,Diff_pvmOptions::getInstance().debuglevel.value());
-
+
LSMCMCManager lsmcmc(Diff_pvmOptions::getInstance(),model,data,mask);
LSLaplaceManager lslaplace(Diff_pvmOptions::getInstance(),model,data,mask);
-
-
+
+
if(Diff_pvmOptions::getInstance().inference.value()=="mcmc")
{
lsmcmc.setup();
lsmcmc.run();
+ element_mod_n(lsmcmc.getsamples(0),M_PI);
+ element_mod_n(lsmcmc.getsamples(1),2*M_PI);
lsmcmc.save();
+
}
else
{
diff --git a/old_bedpost b/old_bedpost
index f0a7b71..7b4ff61 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -20,8 +20,7 @@ Clean_Exit(){
for j in ${i};do
host=`echo $j | awk -F _fdt_ '{print $1}'`
pid=`echo $j | awk -F _fdt_ '{print $2}'`
- echo ${pid}
- if [ x${FSL_MACHINE_LIST} != "x" ]; then
+ if [ "x${FSL_MACHINE_LIST}" != "x" ]; then
# ${FSL_REMOTE_CALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
$FSL_REMOTE_CALL $host "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" >/dev/null 2>&1 &
else
@@ -34,7 +33,7 @@ Clean_Exit(){
}
Lock(){
- if [ x${FSL_LOCK_DIR} != "x" ];then
+ if [ "x${FSL_LOCK_DIR}" != "x" ];then
touch ${FSL_LOCK_DIR}/.bedpost.lock
fi
}
@@ -48,18 +47,18 @@ ExitUnlock(){
ndat_sl=`echo ${subjdir}/data_slice_* | grep -v "slice_\*" |wc -w`
nnodif_sl=`echo ${subjdir}/nodif_brain_mask_slice_* | grep -v "slice_\*" |wc -w`
if [ $ndat_sl -ge 0 ] ;then
- echo "rm -f ${subjdir}/data_slice_*"
+ rm -f ${subjdir}/data_slice_*
fi
if [ $nnodif_sl -ge 0 ] ;then
- echo "rm -f ${subjdir}/nodif_brain_mask_slice_*"
+ rm -f ${subjdir}/nodif_brain_mask_slice_*
fi
exit
}
LockTest(){
- if [ x${FSL_LOCK_DIR} = "x" ];then
+ if [ "x${FSL_LOCK_DIR}" = "x" ];then
echo 1;
elif [ ! -e ${FSL_LOCK_DIR}/.bedpost.lock ];then
echo 1;
@@ -185,9 +184,9 @@ done
##this will have to change..
echo "Merging outputs into 4D files"
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples.hdr.gz`
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples.hdr.gz`
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples.hdr.gz`
+${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
+${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
+${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
diff --git a/old_bedpost_proc b/old_bedpost_proc
index 6f77a27..738f103 100755
--- a/old_bedpost_proc
+++ b/old_bedpost_proc
@@ -15,16 +15,16 @@ Usage() {
subjdir=$1
nslices=$2
-## Do the zeropadding tim
+
slice=0
while [ $slice -lt $nslices ];do
- slicezp=`zeropad $slice 4`
+ slicezp=`${FSLDIR}/bin/zeropad $slice 4`
if [ ! -e ${subjdir}.bedpost/logs/.$slicezp ] ; then
echo `hostname`_${$} > ${subjdir}.bedpost/logs/.$slicezp
sleep 10
if [ `hostname`_${$} = `cat ${subjdir}.bedpost/logs/.$slicezp | sed -n '1p'` ] ; then
- nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slicezp --mask=${subjdir}/nodif_brain_mask_slice_$slicezp -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slicezp --nj=2 --bi=0 --se=1 > ${subjdir}.bedpost/logs/log$slicezp
+ nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slicezp --mask=${subjdir}/nodif_brain_mask_slice_$slicezp -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slicezp --nj=1300 --bi=300 --se=20 > ${subjdir}.bedpost/logs/log$slicezp
touch ${subjdir}.bedpost/logs/.${slicezp}_finished
fi
fi
--
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