From d39dd0d3914696b819f589ad535588c73bd1a7b9 Mon Sep 17 00:00:00 2001
From: Saad Jbabdi <saad@fmrib.ox.ac.uk>
Date: Tue, 2 May 2006 08:32:14 +0000
Subject: [PATCH] added an option --pd to probtrackx for balancing the
probability w.r.t distance
---
probtrackxOptions.h | 24 ++++++++++++++----------
streamlines.cc | 22 +++++++++++++++++-----
2 files changed, 31 insertions(+), 15 deletions(-)
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 32ad71c..36431e5 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -35,6 +35,7 @@ class probtrackxOptions {
Option<string> mode;
Option<string> targetfile;
Option<bool> simpleout;
+ Option<int> pathdist;
Option<bool> s2tout;
FmribOption<bool> matrix1out;
FmribOption<bool> matrix2out;
@@ -109,6 +110,9 @@ class probtrackxOptions {
simpleout(string("--opd"), false,
string("output path distribution"),
false, no_argument),
+ pathdist(string("--pd"), 1,
+ string("path distribution, 1:probability,2:distance corrected value"),
+ false, requires_argument),
s2tout(string("--os2t"), false,
string("output seeds to targets"),
false, no_argument),
@@ -119,18 +123,17 @@ class probtrackxOptions {
string("output matrix2"),
false, no_argument),
maskmatrixout(string("--omaskmatrix"), false,
- string("output maskmatrix"),
- false, no_argument),
-
- outfile(string("-o,--out"), string(""),
- string("Output file (only for single seed voxel mode)"),
- false, requires_argument),
+ string("output maskmatrix"),
+ false, no_argument),
+ outfile(string("-o,--out"), string(""),
+ string("Output file (only for single seed voxel mode)"),
+ false, requires_argument),
rubbishfile(string("--rubbish"), string(""),
- string("Rubbish file"),
- false, requires_argument),
+ string("Rubbish file"),
+ false, requires_argument),
seeds_to_dti(string("--xfm"), string(""),
- string("Transform Matrix taking seed space to DTI space default is to use the identity"),false, requires_argument),
- skipmask(string("--no_integrity"), string(""),
+ string("Transform Matrix taking seed space to DTI space default is to use the identity"),false, requires_argument),
+ skipmask(string("--no_integrity"), string(""),
string("no explanation needed"),
false, requires_argument),
seedref(string("--seedref"), string(""),
@@ -205,6 +208,7 @@ class probtrackxOptions {
options.add(logdir);
options.add(forcedir);
options.add(simpleout);
+ options.add(pathdist);
options.add(s2tout);
options.add(matrix1out);
options.add(matrix2out);
diff --git a/streamlines.cc b/streamlines.cc
index f845479..330b214 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -363,11 +363,23 @@ namespace TRACT{
void Counter::update_pathdist(){
const vector<ColumnVector>& path=m_stline.get_path_ref();
- for(unsigned int i=0;i<path.size();i++){
- int x_s=int(round(float(path[i](1)))),y_s=int(round(float(path[i](2)))),z_s=int(round(float(path[i](3))));
- if(m_beenhere(x_s,y_s,z_s)==0){
- m_prob(x_s,y_s,z_s)+=1;
- m_beenhere(x_s,y_s,z_s)=1;
+ if(opts.pathdist.value()==1){
+ for(unsigned int i=0;i<path.size();i++){
+ int x_s=int(round(float(path[i](1)))),y_s=int(round(float(path[i](2)))),z_s=int(round(float(path[i](3))));
+ if(m_beenhere(x_s,y_s,z_s)==0){
+ m_prob(x_s,y_s,z_s)+=1;
+ m_beenhere(x_s,y_s,z_s)=1;
+ }
+ }
+ }
+ else{
+ int d=1;
+ for(unsigned int i=0;i<path.size();i++){
+ int x_s=int(round(float(path[i](1)))),y_s=int(round(float(path[i](2)))),z_s=int(round(float(path[i](3))));
+ if(m_beenhere(x_s,y_s,z_s)==0){
+ m_prob(x_s,y_s,z_s)+=d;d++;
+ m_beenhere(x_s,y_s,z_s)=1;
+ }
}
}
--
GitLab