From 2aac03954ba278665926f5f91367c1b5d77796d2 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Thu, 17 Feb 2011 12:37:11 +0000
Subject: [PATCH] remove temp changes that sneaked in
---
probtrackxOptions.h | 8 +++++++-
streamlines.cc | 23 +----------------------
2 files changed, 8 insertions(+), 23 deletions(-)
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 711da7a..3d0a3f3 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -62,6 +62,7 @@ class probtrackxOptions {
Option<int> nparticles;
Option<int> nsteps;
Option<float> distthresh;
+ FmribOption<float> distthresh3;
Option<float> c_thr;
FmribOption<float> fibthresh;
Option<bool> sampvox;
@@ -75,6 +76,7 @@ class probtrackxOptions {
Option<bool> seedcountastext;
FmribOption<bool> splitmatrix2;
+
void parse_command_line(int argc, char** argv,Log& logger);
void modecheck();
void modehelp();
@@ -182,7 +184,7 @@ class probtrackxOptions {
string("\tFreesurfer-type surface descriptor (in ascii format)"),
false, requires_argument),
meshspace(string("--meshspace"), string("freesurfer"),
- string("Mesh reference space - either 'freesurfer' (default) or 'caret'"),
+ string("Mesh reference space - either 'freesurfer' (default) or 'caret' or 'first'"),
false, requires_argument),
lrmask(string("--lrmask"), string(""),
string("Low resolution binary brain mask for storing connectivity distribution in matrix2 mode"),
@@ -202,6 +204,9 @@ class probtrackxOptions {
distthresh(string("--distthresh"), 0,
string("Discards samples shorter than this threshold (in mm - default=0)"),
false, requires_argument),
+ distthresh3(string("--distthresh3"), 0,
+ string("Discards samples (in matrix3) shorter than this threshold (in voxels - default=0)"),
+ false, requires_argument),
c_thr(string("-c,--cthr"), 0.2,
string("Curvature threshold - default=0.2"),
false, requires_argument),
@@ -277,6 +282,7 @@ class probtrackxOptions {
options.add(nparticles);
options.add(nsteps);
options.add(distthresh);
+ options.add(distthresh3);
options.add(c_thr);
options.add(fibthresh);
options.add(sampvox);
diff --git a/streamlines.cc b/streamlines.cc
index d12c3a5..5e773eb 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -483,13 +483,6 @@ namespace TRACT{
m_SeedRow=1;
- // where we initialise the vector that stores average path lengths
- // (maybe in the future, we shouldn't need --os2t to do this...)
- if(opts.pathlengths.value()){
- m_pathlengths.ReSize(m_numseeds,opts.nparticles.value());
- m_pathlengths = -1.0;
- m_nsamp=1;
- }
}
@@ -638,9 +631,8 @@ namespace TRACT{
if(opts.matrix2out.value()){
next_matrix2_row();
}
- if(opts.seedcountastext.value() || opts.pathlengths.value()){
+ if(opts.seedcountastext.value()){
m_SeedRow++;
- m_nsamp=1;
}
}
@@ -690,15 +682,6 @@ namespace TRACT{
}
}
- if(opts.pathlengths.value()){
- float pathlength=0.0;
- for(unsigned int i=0;i<m_path.size();i++){
- pathlength+=opts.steplength.value();
- }
- m_pathlengths(m_SeedRow,m_nsamp)=pathlength;
- m_nsamp++;
- }
-
}
@@ -905,10 +888,6 @@ namespace TRACT{
void Counter::save_pathdist(){
m_prob.setDisplayMaximumMinimum(m_prob.max(),m_prob.min());
save_volume(m_prob,logger.appendDir(opts.outfile.value()));
-
- if(opts.pathlengths.value()){
- write_ascii_matrix(m_pathlengths,logger.appendDir("pathlengths"));
- }
}
void Counter::save_pathdist(string add){ //for simple mode
--
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