From 04635c65da66f82c5a5f011eeca2668a6753c38d Mon Sep 17 00:00:00 2001
From: Christian Beckmann <c.beckmann@donders.ru.nl>
Date: Mon, 6 Jul 2009 22:20:33 +0000
Subject: [PATCH] added full data normalisation
---
fsl_glm.cc | 25 ++++++++++++++-----------
1 file changed, 14 insertions(+), 11 deletions(-)
diff --git a/fsl_glm.cc b/fsl_glm.cc
index fc2f1b9..c4f1bea 100644
--- a/fsl_glm.cc
+++ b/fsl_glm.cc
@@ -22,8 +22,8 @@ using namespace std;
// The two strings below specify the title and example usage that is
// printed out as the help or usage message
- string title=string("fsl_glm (Version 1.05)")+
- string("\nCopyright(c) 2004-2008, University of Oxford (Christian F. Beckmann)\n")+
+ string title=string("fsl_glm (Version 1.1)")+
+ string("\nCopyright(c) 2004-2009, University of Oxford (Christian F. Beckmann)\n")+
string(" \n Simple GLM usign ordinary least-squares (OLS) regression on\n")+
string(" time courses and/or 3D/4D imges against time courses \n")+
string(" or 3D/4D images\n\n");
@@ -54,6 +54,9 @@ using namespace std;
Option<bool> normdes(string("--des_norm"),FALSE,
string("switch on normalisation of the design matrix columns to unit std. deviation"),
false, no_argument);
+ Option<bool> normdat(string("--dat_norm"),FALSE,
+ string("switch on normalisation of the data time series to unit std. deviation"),
+ false, no_argument);
Option<bool> perfvn(string("--vn"),FALSE,
string(" perform MELODIC variance-normalisation on data"),
false, no_argument);
@@ -161,14 +164,17 @@ int setup(){
data = tmpdata.matrix(mask);
voxels = data.Ncols();
- if(perf_demean.value())
- data = remmean(data,1);
- if(perfvn.value())
- vnscales = Melodic::varnorm(data);
}
else
data = read_ascii_matrix(fnin.value());
+ if(perf_demean.value())
+ data = remmean(data,1);
+ if(perfvn.value())
+ vnscales = Melodic::varnorm(data);
+ if(normdat.value())
+ data = SP(data,ones(data.Nrows(),1)*pow(stdev(data,1),-1));
+
if(fsl_imageexists(fndesign.value())){//read design
volume4D<float> tmpdata;
read_volume4D(tmpdata,fndesign.value());
@@ -183,11 +189,7 @@ int setup(){
}
meanR=mean(data,1);
- if(perf_demean.value()){
- data = remmean(data,1);
- design = remmean(design,1);
- }
-
+ if(perf_demean.value()){
if(normdes.value())
design = SP(design,ones(design.Nrows(),1)*pow(stdev(design,1),-1));
@@ -256,6 +258,7 @@ int main(int argc,char *argv[]){
options.add(fnftest);
options.add(dofset);
options.add(normdes);
+ options.add(normdat);
options.add(perfvn);
options.add(perf_demean);
options.add(help);
--
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