From 0805401d230265ccb48fb489733f0a6bbf30f9ef Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Wed, 19 Dec 2007 17:37:41 +0000
Subject: [PATCH] Made changes for neurological fix - DO NOT MAKE STABLE YET
---
ccopsOptions.h | 1 +
commonopts.h | 17 +++++++++++++++++
dtifitOptions.h | 2 ++
probtrackOptions.h | 1 +
probtrackxOptions.h | 1 +
pt_alltracts.cc | 2 +-
pt_matrix.cc | 6 +++---
pt_matrix_mesh.cc | 4 ++--
pt_seeds_to_targets.cc | 2 +-
pt_simple.cc | 2 +-
pt_twomasks.cc | 4 ++--
streamlines.cc | 2 +-
tractOptions.h | 1 +
vecreg.cc | 2 +-
14 files changed, 35 insertions(+), 12 deletions(-)
create mode 100644 commonopts.h
diff --git a/ccopsOptions.h b/ccopsOptions.h
index 833efdc..9732fcf 100644
--- a/ccopsOptions.h
+++ b/ccopsOptions.h
@@ -15,6 +15,7 @@
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
+#include "commonopts.h"
using namespace Utilities;
namespace CCOPS {
diff --git a/commonopts.h b/commonopts.h
new file mode 100644
index 0000000..beeb06e
--- /dev/null
+++ b/commonopts.h
@@ -0,0 +1,17 @@
+/* commonopts.h
+
+ Mark Jenkinson and Dave Flitney, FMRIB Image Analysis Group
+
+ Copyright (C) 2007 University of Oxford */
+
+/* CCOPYRIGHT */
+
+#if !defined(commonopts_h)
+#define commonopts_h
+
+using std::string;
+using std::cerr;
+using std::cout;
+using std::endl;
+
+#endif
diff --git a/dtifitOptions.h b/dtifitOptions.h
index b29848c..024fc80 100644
--- a/dtifitOptions.h
+++ b/dtifitOptions.h
@@ -15,7 +15,9 @@
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
+#include "commonopts.h"
//#include "newmatall.h"
+
using namespace Utilities;
namespace DTIFIT {
diff --git a/probtrackOptions.h b/probtrackOptions.h
index 4717d61..4590454 100644
--- a/probtrackOptions.h
+++ b/probtrackOptions.h
@@ -16,6 +16,7 @@
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"
+#include "commonopts.h"
//#include "newmatall.h"
using namespace Utilities;
diff --git a/probtrackxOptions.h b/probtrackxOptions.h
index 92a89a0..688d2a2 100644
--- a/probtrackxOptions.h
+++ b/probtrackxOptions.h
@@ -16,6 +16,7 @@
#include <stdio.h>
#include "utils/options.h"
#include "utils/log.h"
+#include "commonopts.h"
//#include "newmatall.h"
using namespace Utilities;
diff --git a/pt_alltracts.cc b/pt_alltracts.cc
index d297f9a..dda056d 100644
--- a/pt_alltracts.cc
+++ b/pt_alltracts.cc
@@ -65,7 +65,7 @@ void alltracts(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
diff --git a/pt_matrix.cc b/pt_matrix.cc
index 4c78d25..bdc3b68 100644
--- a/pt_matrix.cc
+++ b/pt_matrix.cc
@@ -152,7 +152,7 @@ void matrix2(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
@@ -386,7 +386,7 @@ void matrix1(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
@@ -605,7 +605,7 @@ void maskmatrix(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
diff --git a/pt_matrix_mesh.cc b/pt_matrix_mesh.cc
index 2220375..fad1423 100644
--- a/pt_matrix_mesh.cc
+++ b/pt_matrix_mesh.cc
@@ -140,7 +140,7 @@ void mesh_matrix2(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
@@ -330,7 +330,7 @@ void mesh_lengths(){
}
Matrix Seeds_to_DTI;
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value()); // Here seeds_to_dti should take the standard volume to diff space
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value()); // Here seeds_to_dti should take the standard volume to diff space
float lcrat=5;
volume4D<float> loopcheck((int)ceil(mask.xsize()/lcrat)+1,(int)ceil(mask.ysize()/lcrat)+1,(int)ceil(mask.zsize()/lcrat)+1,3);
diff --git a/pt_seeds_to_targets.cc b/pt_seeds_to_targets.cc
index 4193840..57ba00c 100644
--- a/pt_seeds_to_targets.cc
+++ b/pt_seeds_to_targets.cc
@@ -90,7 +90,7 @@ void seeds_to_targets()
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
diff --git a/pt_simple.cc b/pt_simple.cc
index ea90070..1bafb24 100644
--- a/pt_simple.cc
+++ b/pt_simple.cc
@@ -35,7 +35,7 @@ void track(){
if(opts.seedref.value()!=""){
read_volume(prob,opts.seedref.value());
beenhere=prob*0;
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
prob=mask;
diff --git a/pt_twomasks.cc b/pt_twomasks.cc
index f2b721e..2d6cd55 100644
--- a/pt_twomasks.cc
+++ b/pt_twomasks.cc
@@ -75,7 +75,7 @@ void twomasks_symm(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
@@ -315,7 +315,7 @@ void waypoints(){
Matrix Seeds_to_DTI;
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(Seeds_to_DTI,opts.seeds_to_dti.value());
+ Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
Seeds_to_DTI=Identity(4);
diff --git a/streamlines.cc b/streamlines.cc
index 59f38d9..6ecbf8b 100644
--- a/streamlines.cc
+++ b/streamlines.cc
@@ -61,7 +61,7 @@ namespace TRACT{
}
}
if(opts.seeds_to_dti.value()!=""){
- read_ascii_matrix(m_Seeds_to_DTI,opts.seeds_to_dti.value());
+ m_Seeds_to_DTI = read_ascii_matrix(opts.seeds_to_dti.value());
}
else{
m_Seeds_to_DTI=Identity(4);
diff --git a/tractOptions.h b/tractOptions.h
index 3fbab83..8ae5f67 100644
--- a/tractOptions.h
+++ b/tractOptions.h
@@ -15,6 +15,7 @@
#include <stdlib.h>
#include <stdio.h>
#include "utils/options.h"
+#include "commonopts.h"
//#include "newmatall.h"
using namespace Utilities;
diff --git a/vecreg.cc b/vecreg.cc
index 0160ed8..7486124 100755
--- a/vecreg.cc
+++ b/vecreg.cc
@@ -219,7 +219,7 @@ int do_vecreg(){
volumeinfo vinfo;
if((matrix.set())){
- read_ascii_matrix(Aff,matrix.value());
+ Aff = read_ascii_matrix(matrix.value());
}
if((warp.set())){
if(verbose.value()) cerr << "Loading warpfield" << endl;
--
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