diff --git a/Makefile b/Makefile
index c13823298dd7cab7716a99d2d3bc6388c57ff093..812a06e653dd59a389bcac087369b18db5d4135d 100644
--- a/Makefile
+++ b/Makefile
@@ -11,7 +11,7 @@ DLIBS = -lmeshclass -lbint -lnewimage -lutils -lmiscmaths -lnewmat -lnewran -lfs
DTIFIT=dtifit
CCOPS=ccops
-PT=probtrack
+PT=probtrack_old
PTX=probtrackx
FTB=find_the_biggest
PJ=proj_thresh
@@ -27,7 +27,6 @@ INDEXER=indexer
TEST=testfile
VECREG=vecreg
-
DTIFITOBJS=dtifit.o dtifitOptions.o
CCOPSOBJS=ccops.o ccopsOptions.o
PTOBJS=probtrack.o probtrackOptions.o pt_alltracts.o pt_matrix.o pt_seeds_to_targets.o pt_simple.o pt_twomasks.o pt_matrix_mesh.o
@@ -49,17 +48,17 @@ VECREGOBJS=vecreg.o
SGEBEDPOST = bedpost bedpost_datacheck
SGEBEDPOSTX = bedpostx bedpostx_postproc.sh bedpostx_preproc.sh bedpostx_single_slice.sh
-SCRIPTS = eddy_correct zeropad maskdyads ${SGEBEDPOST} ${SGEBEDPOSTX}
+SCRIPTS = eddy_correct zeropad maskdyads probtrack ${SGEBEDPOST} ${SGEBEDPOSTX}
FSCRIPTS = correct_and_average ocmr_preproc
-XFILES = dtifit ccops probtrack find_the_biggest medianfilter diff_pvm make_dyadic_vectors proj_thresh vecreg xfibres
+XFILES = dtifit ccops find_the_biggest medianfilter diff_pvm make_dyadic_vectors proj_thresh vecreg xfibres probtrackx
-FXFILES = reord_OM sausages replacevols fdt_matrix_ops probtrackx indexer
+FXFILES = reord_OM sausages replacevols fdt_matrix_ops indexer
RUNTCLS = Fdt
-all: ${XFILES} ${FXFILES}
+all: ${XFILES} ${FXFILES} probtrack_old
${PTX}: ${PTXOBJS}
${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${PTXOBJS} ${DLIBS}
diff --git a/doc/index.html b/doc/index.html
index 1122a2fb80aba8a74aba0f1918e3f92bb53c4d3f..d8b4fdb17d32ce02ddf3286ad7976e7e908e999b 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -5,3 +5,4 @@
<frame name="dynamic" src="fdt_intro.html" marginwidth="10" marginheight="10" frameborder="no">
<frame src="fdt_bottom.html" marginwidth="10" marginheight="10" frameborder="no">
</frameset>
+
diff --git a/fdt.tcl b/fdt.tcl
index 5560cdfea977ff57333c70fc9d12e5cc13a150fd..a98afd2b0936f0537e9416f8481c09a56060a19b 100644
--- a/fdt.tcl
+++ b/fdt.tcl
@@ -237,14 +237,13 @@ proc fdt:dialog { w tclstartupfile } {
FileEntry $w.data.seed.ssf.xfm -textvariable probtrack(xfm) -label "Select Seed to diff transform" -title "Select seed-space to DTI-space transformation matrix" -filetypes *
pack $w.data.seed.ssf.ssd -side top -anchor nw
-
-
-
- frame $w.data.seed.bcf
- checkbutton $w.data.seed.bcf.bc -text "Blind Classification:" -variable probtrack(bcyn) -command " pack forget $w.data.seed.bcf.w ; if { \$probtrack(bcyn) } { pack $w.data.seed.bcf.w -side left} ; $w.probtrack compute_size"
- set probtrack(scale) 5
- LabelSpinBox $w.data.seed.bcf.w -label "Low resolution rescaling factor" -textvariable probtrack(scale) -range {1 1000000 1 }
- pack $w.data.seed.bcf.bc -side left -anchor w
+ if { [ file exists /usr/local/fsl/bin/reord_OM ] } {
+ frame $w.data.seed.bcf
+ checkbutton $w.data.seed.bcf.bc -text "Blind Classification:" -variable probtrack(bcyn) -command " pack forget $w.data.seed.bcf.w ; if { \$probtrack(bcyn) } { pack $w.data.seed.bcf.w -side left} ; $w.probtrack compute_size"
+ set probtrack(scale) 5
+ LabelSpinBox $w.data.seed.bcf.w -label "Low resolution rescaling factor" -textvariable probtrack(scale) -range {1 1000000 1 }
+ pack $w.data.seed.bcf.bc -side left -anchor w
+ }
pack $w.data.seed.voxel.x $w.data.seed.voxel.y $w.data.seed.voxel.z $w.data.seed.voxel.vox $w.data.seed.voxel.mm -side left -padx 2
pack $w.data.seed.voxel $w.data.seed.ssf -in $w.data.seed.f -side bottom -anchor w -pady 2
@@ -468,10 +467,13 @@ proc fdt:probtrack_mode { w } {
$w.data.dir configure -label "Output file:" -title "Name the output file" -filetypes IMAGE
}
seedmask {
- pack $w.data.seed.ssf $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2
- pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
- pack $w.data.targets.cf -in $w.data.targets.f -anchor w
- $w.data.seed.reference configure -label "Mask image:" -title "Choose mask image"
+ pack $w.data.seed.ssf -in $w.data.seed.f -side bottom -anchor w -pady 2
+ if { [ file exists /usr/local/fsl/bin/reord_OM ] } {
+ pack $w.data.seed.bcf -in $w.data.seed.f -side bottom -anchor w -pady 2
+ }
+ pack $w.data.seed.menu $w.data.seed.reference -in $w.data.seed.f -side left -anchor w -pady 2
+ pack $w.data.targets.cf -in $w.data.targets.f -anchor w
+ $w.data.seed.reference configure -label "Mask image:" -title "Choose mask image"
}
network {
pack $w.data.seed.target $w.data.seed.ssf $w.data.seed.menu -in $w.data.seed.f -side bottom -anchor w -pady 2
diff --git a/fibre.h b/fibre.h
index 6a3220710c9a0368e0d8c02317ff9418e0c6a6b0..8aca32d8401f61909a717b44dbc1053ae8c938d2 100644
--- a/fibre.h
+++ b/fibre.h
@@ -91,7 +91,6 @@ namespace FIBRE{
m_f_prior=0;
compute_f_prior();
- //cc OUT("COCK1");
//cc OUT(m_f_prior);
//cc OUT(m_ardfudge);
m_lam_prior=0;
@@ -134,7 +133,6 @@ namespace FIBRE{
m_f_prior=0;
compute_f_prior();
- //cc OUT("COCK2");
//cc OUT(m_f_prior);
//cc OUT(m_ardfudge);
m_lam_prior=0;
diff --git a/probtrack b/probtrack
new file mode 100755
index 0000000000000000000000000000000000000000..de48dd6b72db8a5f6f083f73645fb7fe1303c8f1
--- /dev/null
+++ b/probtrack
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+# Copyright (C) 2007 University of Oxford
+#
+# SHCOPYRIGHT
+
+echo
+echo "Error - probtrack has been superceded by probtrackx!"
+echo "Please see the FDT documentation for the new probtrackx syntax"
+echo
+
diff --git a/replacevols.cc b/replacevols.cc
index e728cd8defeaf78f5eb97e91c9a2132df2df8c5b..1173c176d6187ef47bf4495d8cd8ed93756939f4 100644
--- a/replacevols.cc
+++ b/replacevols.cc
@@ -12,16 +12,16 @@ int read_avg_file (vector<vector<int> >& avgs,const string fname){
avgs.clear();
ifstream avg_file(fname.c_str());
string myline;
- bool cocksize=true;
+ bool nobbsize=true;
int row = 0;
if(!avg_file){return -1;}
else{
- while(cocksize){
+ while(nobbsize){
avgs.push_back(vector<int>());
- cocksize=false;
+ nobbsize=false;
getline(avg_file,myline);
int pos=0;
@@ -42,7 +42,7 @@ int read_avg_file (vector<vector<int> >& avgs,const string fname){
int length;
mylinestr >> startstr;
if(isnum(startstr)){
- cocksize=true;
+ nobbsize=true;
start = atoi(startstr.c_str());
mylinestr >> length;
diff --git a/xfibres.cc b/xfibres.cc
index e212ac9c34075500b83bc15f0791f1748405612c..3086ed0feade625c6bf29825beebe743454ad4b9 100644
--- a/xfibres.cc
+++ b/xfibres.cc
@@ -278,9 +278,9 @@ public:
m_sum_lam[f]=0;
}
m_beenhere(int(m_matrix2volkey(vox,1)),int(m_matrix2volkey(vox,2)),int(m_matrix2volkey(vox,3)))=nfibs;
- cout<<nfibs<<endl;
- cout <<"boobooboo"<<endl;
- cout<<int(m_matrix2volkey(vox,1))<<" "<<int(m_matrix2volkey(vox,2))<<" "<<int(m_matrix2volkey(vox,3))<<endl;
+ //cout<<nfibs<<endl;
+ //cout <<"boobooboo"<<endl;
+ //cout<<int(m_matrix2volkey(vox,1))<<" "<<int(m_matrix2volkey(vox,2))<<" "<<int(m_matrix2volkey(vox,3))<<endl;
}