diff --git a/old_bedpost b/old_bedpost
index e8a8b74abb8046f955a89837d62c8a8cd30a3b17..54519820b35d69a4deae6b22e7238f3e7928326c 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -2,36 +2,80 @@
Usage() {
echo ""
- echo "Usage: Bedpost <subject directory> "
+ echo "Usage: bedpost <subject directory> "
echo ""
echo "expects to find bvals and bvecs in subject directory"
echo "expects to find data nodif_brain_mask nodif in subject directory"
- echo "N.B. nodif_brain_mask has to be betted"
echo ""
- echo "If struct is in subject directory transforms will be made"
- echo "NB: if there, struct should already be betted"
exit
}
-ExitUnlock() {
- rm /usr/people/dtiuser/locks/.bedpost.lock
+trap Clean_Exit 2
+
+
+Clean_Exit(){
+
+ if [ -d ${subjdir}.bedpost/logs/pid_${$} ];then
+ i=`ls ${subjdir}.bedpost/logs/pid_${$}`
+ for j in ${i};do
+ host=`echo $j | awk --field-separator=_fdt_ '{print $1}'`
+ pid=`echo $j | awk --field-separator=_fdt_ '{print $2}'`
+ ${FSL_REMOTE_CALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
+ done
+ fi
+
+ ExitUnlock;
+}
+
+Lock(){
+ if [ x${FSL_LOCK_DIR} != "x" ];then
+ touch ${FSL_LOCK_DIR}/.bedpost.lock
+ fi
+}
+
+ExitUnlock(){
+ if [ -e ${FSL_LOCK_DIR}/.bedpost.lock ];then
+ rm ${FSL_LOCK_DIR}/.bedpost.lock
+ fi
exit
}
+LockTest(){
+ if [ x${FSL_LOCK_DIR} = "x" ];then
+ echo 1;
+ elif [ ! -e ${FSL_LOCK_DIR}/.bedpost.lock ];then
+ echo 1;
+ else
+ echo 0;
+ fi
+}
+
+make_absolute(){
+ dir=$1;
+ if [ -d ${dir} ]; then
+ OLDWD=`pwd`
+ cd ${dir}
+ dir_all=`pwd`
+ cd $OLDWD
+ else
+ dir_all=${dir}
+ fi
+ echo ${dir_all}
+}
-[ "$1" = "" ] && Usage
-if [ -e /usr/people/dtiuser/locks/.bedpost.lock ]; then
+[ "$1" = "" ] && Usage
+
+if [ `LockTest` -eq 0 ]; then
echo "bedpost is currently being run - try again later"
exit
fi
-touch /usr/people/dtiuser/locks/.bedpost.lock
+Lock();
-projdir=`pwd`
-subjdir=`basename $1`
-subjdir=${projdir}/${subjdir}
+subjdir=`make_absolute $1`
+subjdir=`echo $subjdir | sed 's/\/$/$/g'`
echo subjectdir is $subjdir
@@ -52,60 +96,39 @@ if [ ! -e ${subjdir}/bvals ]; then
ExitUnlock
fi
-if [ ! -e ${subjdir}/data.hdr ]; then
- echo "${subjdir}/data.hdr not found"
+if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
+ echo "${subjdir}/data not found"
ExitUnlock
fi
-if [ ! -e ${subjdir}/nodif.hdr ]; then
- echo "${subjdir}/nodif.hdr not found"
+if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` -eq 0 ]; then
+ echo "${subjdir}/nodif not found"
ExitUnlock
fi
-if [ ! -e ${subjdir}/nodif_brain_mask.hdr ]; then
- echo "${subjdir}/nodif_brain_mask.hdr not found"
+if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
+ echo "${subjdir}/nodif_brain_mask not found"
ExitUnlock
fi
-if [ ! -e ${subjdir}/data.img ]; then
- echo "${subjdir}/data.img not found"
- ExitUnlock
-fi
-
-if [ ! -e ${subjdir}/nodif.img ]; then
- echo "${subjdir}/nodif.img not found"
- ExitUnlock
-fi
-
-if [ ! -e ${subjdir}/nodif_brain_mask.img ]; then
- echo "${subjdir}/nodif_brain_mask.img not found"
- ExitUnlock
-fi
-
-
-
echo making bedpost directory
-mkdir ${subjdir}.bedpost/
-mkdir ${subjdir}.bedpost/diff_slices
+mkdir -p ${subjdir}.bedpost/
+mkdir -p ${subjdir}.bedpost/diff_slices
echo copying files to bedpost directory
-cp ${subjdir}/bvecs ${subjdir}.bedpost
-cp ${subjdir}/bvals ${subjdir}.bedpost
-cp ${subjdir}/nodif.hdr ${subjdir}.bedpost
-cp ${subjdir}/nodif.img ${subjdir}.bedpost
-cp ${subjdir}/nodif_brain_mask.hdr ${subjdir}.bedpost
-cp ${subjdir}/nodif_brain_mask.img ${subjdir}.bedpost
-
+cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpost
+${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpost
mkdir -p ${subjdir}.bedpost/logs
+mkdir -p ${subjdir}.bedpost/logs/pid_${$}
nslices=`avwval ${subjdir}/data dim3`
-${FSLDIR}/bin/avwslice ${subjdir}/data
-${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
+#${FSLDIR}/bin/avwslice ${subjdir}/data
+#${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
#following need to be setup elsewhere
#FSL_MACHINE_LIST="cayenne0 cayenne0 cayenne2 cayenne3"
@@ -115,16 +138,23 @@ if [ "$FSL_MACHINE_LIST" = "" ] ; then
${FSLDIR}/bin/bedpost_proc $subjdir $nslices
else
for machine in $FSL_MACHINE_LIST; do
- $FSL_REMOTE_CALL $machine ${FSLDIR}/bin/bedpost_proc $subjdir $nslices &
+ $FSL_REMOTE_CALL $machine "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_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
done
fi
-echo "DONE"
+finished=0;
+while [ $finished -eq 0 ];do
+ sleep 60;
+ nfin=`ls ${subjdir}.bedpost/logs/.*_finished |wc -w` #fix this (see Bedpost)
+ if [ $nfin -eq $nslices ];then
+ finished=1;
+ fi
+done
+
#postprocessing
#postprocess $subjdir
-
mkdir -p ${subjdir}.bedpost/xfms
xfmdir=${subjdir}.bedpost/xfms
echo 1 0 0 0 > ${xfmdir}/eye.mat
@@ -132,7 +162,11 @@ 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"
+
+ExitUnlock()
+
+
-rm /usr/people/dtiuser/locks/.bedpost.lock
diff --git a/old_bedpost_proc b/old_bedpost_proc
index ee26c49cc7f01048baa9473a3a6b81380bcc48bb..65b4f4570fe911a493ce0b747c6a103306249f0a 100755
--- a/old_bedpost_proc
+++ b/old_bedpost_proc
@@ -2,27 +2,29 @@
Usage() {
echo ""
- echo "Usage: bedpost_proc <subject_dir> <nslices>"
+ echo "Usage: bedpost_proc <subject_dir> <nslices> [piddir]"
echo ""
exit
}
[ "$2" = "" ] && Usage
+[ "$3" = "" ] || touch ${3}/`hostname`_fdt_${$}
subjdir=$1
nslices=$2
-
+
slice=0
while [ $slice -lt $nslices ];do
-
if [ ! -e ${subjdir}.bedpost/logs/.$slice ] ; then
- echo `hostname` > ${subjdir}.bedpost/logs/.$slice
+ echo `hostname`_${$} > ${subjdir}.bedpost/logs/.$slice
sleep 10
- if [ `hostname` = `cat ${subjdir}.bedpost/logs/.$slice` ] ; then
+ if [ `hostname`_${$} = `cat ${subjdir}.bedpost/logs/.$slice` ] ; then
nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slice --mask=${subjdir}/nodif_brain_mask_slice_$slice -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slice --nj=1300 --bi=300 --se=20 > ${subjdir}.bedpost/logs/log$slice
+ touch ${subjdir}.bedpost/logs/.${slice}_finished
fi
fi
slice=`echo "$slice + 1" | bc`
done
-
+[ "$3" = "" ] || rm ${3}/`hostname`_fdt_${$}
+sleep 10
\ No newline at end of file
diff --git a/pt_alltracts.cc b/pt_alltracts.cc
index a74574b6dd297af2bb9fc4106cbe98dde85ec1a6..b7539af3744e97426760d7eb943e16af9f6d10d9 100644
--- a/pt_alltracts.cc
+++ b/pt_alltracts.cc
@@ -142,7 +142,7 @@ void alltracts(){
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
else{
- if(skipmask((int)round(part.x()),(int)round(part.y()),(int)round(part.z()))==0)
+ if(skipmask(x_s,y_s,z_s)==0)
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
diff --git a/pt_matrix.cc b/pt_matrix.cc
index eb167ea4194199cf007573070b561f28d24a27fc..1cbb068913c2537b3e53bca03895267e04dd749c 100644
--- a/pt_matrix.cc
+++ b/pt_matrix.cc
@@ -247,7 +247,7 @@ void matrix2(){
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
else{
- if(skipmask((int)round(part.x()),(int)round(part.y()),(int)round(part.z()))==0)
+ if(skipmask(x_s,y_s,z_s)==0)
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
diff --git a/pt_matrix_mesh.cc b/pt_matrix_mesh.cc
index b37aefd93f8ed8f5d30fd5078d269abdb950690d..acc5165067ff6c77c4f8a5341bfa1ee52d27e8db 100644
--- a/pt_matrix_mesh.cc
+++ b/pt_matrix_mesh.cc
@@ -231,8 +231,14 @@ void mesh_matrix2(){
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
else{
- if(skipmask((int)round(part.x()),(int)round(part.y()),(int)round(part.z()))==0)
+ xyz_rubbish=vox_to_vox(xyz_dti,vols.dimensions(),dim_rubbish,Seeds_to_DTI.i());
+ int x_s =(int)round((float)xyz_rubbish(1));
+ int y_s =(int)round((float)xyz_rubbish(2));
+ int z_s =(int)round((float)xyz_rubbish(3));
+
+ if(skipmask(x_s,y_s,z_s)==0)
th_ph_f=vols.sample(part.x(),part.y(),part.z());
+
}
tmp2=rand(); tmp2/=RAND_MAX;
diff --git a/pt_seeds_to_targets.cc b/pt_seeds_to_targets.cc
index a3a07e5c99ae85c2e85279b086a3db43fbeb1bea..c1690e8b2ab0a056ce14053b4158ec36c53faf88 100644
--- a/pt_seeds_to_targets.cc
+++ b/pt_seeds_to_targets.cc
@@ -172,7 +172,7 @@ void seeds_to_targets()
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
else{
- if(skipmask((int)round(part.x()),(int)round(part.y()),(int)round(part.z()))==0)
+ if(skipmask(x_s,y_s,z_s)==0)
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
diff --git a/pt_twomasks.cc b/pt_twomasks.cc
index b1479a9b3ec97d2f34c83879ab3c8c3f78fefbe7..d00a87574cc763be427573ef89dfd2ecfe2d898c 100644
--- a/pt_twomasks.cc
+++ b/pt_twomasks.cc
@@ -148,7 +148,7 @@ void twomasks_symm(){
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}
else{
- if(skipmask((int)round(part.x()),(int)round(part.y()),(int)round(part.z()))==0)
+ if(skipmask(x_s,y_s,z_s)==0)
th_ph_f=vols.sample(part.x(),part.y(),part.z());
}