From 0194bf4743854c5a9d0dfa1320550606d307ada0 Mon Sep 17 00:00:00 2001
From: Christian Beckmann <c.beckmann@donders.ru.nl>
Date: Mon, 2 Nov 2009 22:05:35 +0000
Subject: [PATCH] added debug messages to fsl_glm
---
fsl_glm.cc | 31 +++++++++++++++++++++++++++----
1 file changed, 27 insertions(+), 4 deletions(-)
diff --git a/fsl_glm.cc b/fsl_glm.cc
index 9a5b54e..f6801cc 100644
--- a/fsl_glm.cc
+++ b/fsl_glm.cc
@@ -155,12 +155,16 @@ int setup(){
// create mask
if(fnmask.value()>""){
+ if(debug.value())
+ cout << "Reading mask file " << fnmask.value() << endl;
read_volume(mask,fnmask.value());
if(!samesize(tmpdata[0],mask)){
cerr << "ERROR: Mask image does not match input image" << endl;
return 1;
};
}else{
+ if(debug.value())
+ cout << "Creating mask image" << endl;
mask=tmpdata[0]*0.0+1.0;
data=tmpdata.matrix(mask);
Melodic::update_mask(mask,data);
@@ -169,6 +173,8 @@ int setup(){
voxels = data.Ncols();
if(perfvn.value()){
+ if(debug.value())
+ cout << "Perform MELODIC variance normalisation (and demeaning)" << endl;
data = remmean(data,1);
vnscales = Melodic::varnorm(data);
}
@@ -177,28 +183,44 @@ int setup(){
data = read_ascii_matrix(fnin.value());
if(fsl_imageexists(fndesign.value())){//read design
+ if(debug.value())
+ cout << "Reading design file "<< fndesign.value()<< endl;
volume4D<float> tmpdata;
read_volume4D(tmpdata,fndesign.value());
if(!samesize(tmpdata[0],mask)){
cerr << "ERROR: GLM design does not match input image in size" << endl;
return 1;
}
+ if(debug.value())
+ cout << "Transposing data" << endl;
design = tmpdata.matrix(mask).t();
data = data.t();
}else{
design = read_ascii_matrix(fndesign.value());
}
- if(perf_demean.value())
+ if(perf_demean.value()){
+ if(debug.value())
+ cout << "De-meaning the data matrix" << endl;
data = remmean(data,1);
- if(normdat.value())
+ }
+ if(normdat.value()){
+ if(debug.value())
+ cout << "Normalising data matrix to unit std-deviation" << endl;
data = SP(data,ones(data.Nrows(),1)*pow(stdev(data,1),-1));
+ }
meanR=mean(data,1);
- if(perf_demean.value())
+ if(perf_demean.value()){
+ if(debug.value())
+ cout << "De-meaning design matrix" << endl;
design = remmean(design,1);
- if(normdes.value())
+ }
+ if(normdes.value()){
+ if(debug.value())
+ cout << "Normalising design matrix to unit std-deviation" << endl;
design = SP(design,ones(design.Nrows(),1)*pow(stdev(design,1),-1));
+ }
if(fncontrasts.value()>""){//read contrast
contrasts = read_ascii_matrix(fncontrasts.value());
if(!(contrasts.Ncols()==design.Ncols())){
@@ -268,6 +290,7 @@ int main(int argc,char *argv[]){
options.add(perfvn);
options.add(perf_demean);
options.add(help);
+ options.add(debug);
options.add(outcope);
options.add(outz);
options.add(outt);
--
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