diff --git a/old_bedpostX b/old_bedpostX
index 7b499c54ce782e1ce8780703772b54c7c02e9a71..00e407c9a1ddf462c68f95eedd54eb69d10cb05c 100644
--- a/old_bedpostX
+++ b/old_bedpostX
@@ -108,21 +108,6 @@ fi
Lock;
-#parse option arguments
-nfibres=2
-fudge=1
-burnin=1000
-while [ ! -z "$2" ]
-do
- case "$2" in
- -n) nfibres=$3;shift;;
- -w) fudge=$3;shift;;
- -b) burnin=$3;shift;;
- *) break;;
- esac
- shift
-done
-
subjdir=`make_absolute $1`
subjdir=`echo $subjdir | sed 's/\/$/$/g'`
@@ -163,6 +148,22 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
fi
+#parse option arguments
+nfibres=2
+fudge=1
+burnin=1000
+while [ ! -z "$2" ]
+do
+ case "$2" in
+ -n) nfibres=$3;shift;;
+ -w) fudge=$3;shift;;
+ -b) burnin=$3;shift;;
+ *) break;;
+ esac
+ shift
+done
+
+
echo making bedpostX directory
mkdir -p ${subjdir}.bedpostX/
mkdir -p ${subjdir}.bedpostX/diff_slices
@@ -216,7 +217,7 @@ done
numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples |wc -w`
-
+echo number of fibres $numfib
fib=1;
while [ $fib -le $numfib ];do
@@ -232,9 +233,6 @@ while [ $fib -le $numfib ];do
fib=`echo "$fib +1"|bc`;
done
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/meanSignal `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/meanSignal`
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/stdSignal `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/stdSignal`
-
echo Removing intermediate files
if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
diff --git a/old_bedpostX_proc b/old_bedpostX_proc
index 56d192ee61a62be7a3e1988839c42fdd8069de9e..54814bc280f5ca5130009fd68d2b5c9e6fa98bb4 100644
--- a/old_bedpostX_proc
+++ b/old_bedpostX_proc
@@ -14,6 +14,11 @@ Usage() {
[ "$2" = "" ] && Usage
+
+subjdir=$1
+nslices=$2
+
+
#parse option arguments
nfibres=2
fudge=1.5
@@ -29,13 +34,16 @@ do
shift
done
+echo subjdir $subjdir
+echo nslices $nslices
+echo nfibres $nfibres
+echo fudge $fudge
+echo burnin $burnin
+echo piddir $piddir
[ "$piddir" = "" ] || touch ${piddir}/`hostname`_fdt_${$}
-subjdir=$1
-nslices=$2
-
slice=0
while [ $slice -lt $nslices ];do
slicezp=`${FSLDIR}/bin/zeropad $slice 4`
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 07724aaa1af3aa60fbdd4178df00f1db86ea45c5..95617682078bf2326fdeb620a4e527eba4d6a565 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -48,6 +48,7 @@ class probtrackxOptions {
Option<string> seedref;
Option<string> mask2;
Option<string> waypoints;
+ Option<bool> waypoints_and;
Option<string> meshfile;
FmribOption<string> lrmask;
Option<string> logdir;
@@ -129,8 +130,8 @@ class probtrackxOptions {
outfile(string("-o,--out"), string(""),
string("Output file (only for single seed voxel mode)"),
false, requires_argument),
- rubbishfile(string("--rubbish"), string(""),
- string("Rubbish file"),
+ rubbishfile(string("--avoid"), string(""),
+ string("Reject pathways passing through locations given by this mask"),
false, requires_argument),
stopfile(string("--stop"), string(""),
string("Stop tracking at locations given by this mask file"),
@@ -147,13 +148,16 @@ class probtrackxOptions {
string("second mask in twomask_symm mode."),
false, requires_argument),
waypoints(string("--waypoints"), string(""),
- string("Waypoint mask or ascii list of waypoint masks."),
- false, requires_argument),
+ string("Waypoint mask or ascii list of waypoint masks"),
+ false, requires_argument),
+ waypoints_and(string("--network"), true,
+ string("Searches for pathways connecting every seed to at least one waypoint"),
+ false, no_argument),
meshfile(string("--mesh"), string(""),
string(""),
false, requires_argument),
lrmask(string("--lrmask"), string(""),
- string("low resolution binary brain mask for stroring connectivity distribution in matrix2 mode."),
+ string("low resolution binary brain mask for stroring connectivity distribution in matrix2 mode"),
false, requires_argument),
logdir(string("--dir"), string(""),
string("Directory to put the final volumes in - code makes this directory"),
@@ -206,6 +210,7 @@ class probtrackxOptions {
options.add(skipmask);
options.add(mask2);
options.add(waypoints);
+ options.add(waypoints_and);
options.add(meshfile);
options.add(lrmask);
options.add(seedref);
diff --git a/streamlines.cc b/streamlines.cc
index 5a4c6d6d7431c1e270a157e82098176a10a823f0..341aa7e5b87c21fa4eee402cee347155b28d2635 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -94,6 +94,7 @@ namespace TRACT{
m_part.change_xyz(x,y,z);
int partlength=0;
bool rubbish_passed=false;
+ bool stop_flag=false;
//NB - this only goes in one direction!!
for(unsigned int pf=0;pf<m_passed_flags.size();pf++) {
m_passed_flags[pf]=false; /// only keep it if this streamline went through all the masks
@@ -150,9 +151,10 @@ namespace TRACT{
}
if(opts.stopfile.value()!=""){
if(m_stop(x_s,y_s,z_s)!=0){
- m_path.pop_back();
- break;
+ stop_flag=true;
}
+ else
+ if(stop_flag)break;
}
diff --git a/xfibres.cc b/xfibres.cc
index 0baed21bf997712b0eee145e53f33692ec0f6d0d..53d4ed1133fefde27c5dbca45ebef1f585d594d8 100644
--- a/xfibres.cc
+++ b/xfibres.cc
@@ -360,12 +360,12 @@ public:
mean_fsamples_out.push_back(m_mean_fsamples[f]);
Log& logger = LogSingleton::getInstance();
- tmp.setmatrix(m_dsamples,mask);
- save_volume4D(tmp,logger.appendDir("dsamples"));
- tmp.setmatrix(m_S0samples,mask);
- save_volume4D(tmp,logger.appendDir("S0samples"));
- tmp.setmatrix(m_lik_energy,mask);
- save_volume4D(tmp,logger.appendDir("lik_energy"));
+ //tmp.setmatrix(m_dsamples,mask);
+ //save_volume4D(tmp,logger.appendDir("dsamples"));
+ //tmp.setmatrix(m_S0samples,mask);
+ //save_volume4D(tmp,logger.appendDir("S0samples"));
+ //tmp.setmatrix(m_lik_energy,mask);
+ //save_volume4D(tmp,logger.appendDir("lik_energy"));
//Sort the output based on mean_fsamples
//