From 672473db06729e832c2202c16b573874b6ef7abe Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Fri, 9 Dec 2011 16:37:16 +0000
Subject: [PATCH] now with static vxt option
---
fsl_glm.cc | 26 +++++++++++++++++++++-----
1 file changed, 21 insertions(+), 5 deletions(-)
diff --git a/fsl_glm.cc b/fsl_glm.cc
index 3d97261..ab9a411 100644
--- a/fsl_glm.cc
+++ b/fsl_glm.cc
@@ -103,8 +103,11 @@ using namespace std;
Option<string> outvnscales(string("--out_vnscales"),string(""),
string("output file name for scaling factors for variance normalisation"),
false, requires_argument);
+ Option<vector<string> > textConfounds(string("--vxt"), vector<string>(),
+ string("\tlist of text files containing text matrix confounds. caution BETA option."),
+ false, requires_argument);
Option<vector<string> > voxelwiseConfounds(string("--vxf"), vector<string>(),
- string("\tlist of 4D images containing voxelwise EVs (list order corresponds to numbers in vxl option). caution BETA option."),
+ string("\tlist of 4D images containing voxelwise confounds. caution BETA option."),
false, requires_argument);
/*
}
@@ -203,11 +206,19 @@ int setup(int &dof){
}
dof=(int)ols_dof(design);
+ Matrix baseConfounds;
+ if ( textConfounds.set() ) {
+ baseConfounds=read_ascii_matrix( textConfounds.value().at(0) );
+ for(unsigned int i=1; i< textConfounds.value().size(); i++)
+ baseConfounds|=read_ascii_matrix( textConfounds.value().at(i) );
+ dof-=textConfounds.value().size();
+ if ( !voxelwiseConfounds.set() )
+ data=(IdentityMatrix(baseConfounds.Nrows())-baseConfounds*pinv(baseConfounds))*data;
+ }
if ( voxelwiseConfounds.set() ) {
vector<Matrix> confounds;
confounds.resize(voxelwiseConfounds.value().size());
- cerr << confounds.size() << endl;
volume4D<float> input;
for(unsigned int i=0; i< confounds.size(); i++) {
read_volume4D(input,voxelwiseConfounds.value().at(i));
@@ -220,11 +231,15 @@ int setup(int &dof){
Matrix confound(confounds.at(0).Column(voxel) );
for(unsigned int i=1; i< confounds.size(); i++)
confound|=confounds.at(i).Column(voxel);
- data.Column(voxel)=(IdentityMatrix(confound.Nrows())-confound*pinv(confound))*data.Column(voxel);
- }
- dof-=2;
+ if ( textConfounds.set() )
+ confound=baseConfounds | confound;
+ data.Column(voxel)=(IdentityMatrix(confound.Nrows())-confound*pinv(confound))*data.Column(voxel);
+ }
+ dof-=confounds.size();
}
+
+
if(perf_demean.value()){
if(debug.value())
cout << "De-meaning the data matrix" << endl;
@@ -329,6 +344,7 @@ int main(int argc,char *argv[]){
options.add(outsigsq);
options.add(outdata);
options.add(outvnscales);
+ options.add(textConfounds);
options.add(voxelwiseConfounds);
options.parse_command_line(argc, argv);
--
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