From fc02942eec173eac5844db01396cbaafe72303ea Mon Sep 17 00:00:00 2001
From: Christian Beckmann <c.beckmann@donders.ru.nl>
Date: Tue, 7 Jul 2009 11:18:03 +0000
Subject: [PATCH] more modifications
---
fsl_glm.cc | 44 +++++++++++++++++++++++++-------------------
1 file changed, 25 insertions(+), 19 deletions(-)
diff --git a/fsl_glm.cc b/fsl_glm.cc
index c4f1bea..9a5b54e 100644
--- a/fsl_glm.cc
+++ b/fsl_glm.cc
@@ -26,7 +26,7 @@ using namespace std;
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");
+ string(" or 3D/4D images");
string examples="fsl_glm -i <input> -d <design> -o <output> [options]";
//Command line Options {
@@ -35,10 +35,10 @@ using namespace std;
true, requires_argument);
Option<string> fnout(string("-o,--out"), string(""),
string("output file name for GLM parameter estimates (GLM betas)"),
- true, requires_argument);
+ false, requires_argument);
Option<string> fndesign(string("-d,--design"), string(""),
string("file name of the GLM design matrix (time courses or spatial maps)"),
- true, requires_argument);
+ false, requires_argument);
Option<string> fnmask(string("-m,--mask"), string(""),
string("mask image file name if input is image"),
false, requires_argument);
@@ -66,6 +66,9 @@ using namespace std;
Option<int> help(string("-h,--help"), 0,
string("display this help text"),
false,no_argument);
+ Option<bool> debug(string("--debug"), FALSE,
+ string("display debug information"),
+ false,no_argument,false);
// Output options
Option<string> outcope(string("--out_cope"),string(""),
string("output file name for COPEs (either as text file or image)"),
@@ -103,7 +106,7 @@ using namespace std;
/*
}
*/
-//Globals {
+//Globals
Melodic::basicGLM glm;
int voxels = 0;
Matrix data;
@@ -112,9 +115,8 @@ using namespace std;
Matrix fcontrasts;
Matrix meanR;
RowVector vnscales;
- volume<float> mask; /*
-}
-*/
+ volume<float> mask;
+
////////////////////////////////////////////////////////////////////////////
// Local functions
@@ -159,22 +161,21 @@ int setup(){
return 1;
};
}else{
- mask = tmpdata[0]*0.0+1.0;
- }
-
+ mask=tmpdata[0]*0.0+1.0;
+ data=tmpdata.matrix(mask);
+ Melodic::update_mask(mask,data);
+ }
data = tmpdata.matrix(mask);
voxels = data.Ncols();
+
+ if(perfvn.value()){
+ data = remmean(data,1);
+ 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());
@@ -188,11 +189,16 @@ int setup(){
design = read_ascii_matrix(fndesign.value());
}
+ if(perf_demean.value())
+ data = remmean(data,1);
+ if(normdat.value())
+ data = SP(data,ones(data.Nrows(),1)*pow(stdev(data,1),-1));
+
meanR=mean(data,1);
- if(perf_demean.value()){
+ if(perf_demean.value())
+ design = remmean(design,1);
if(normdes.value())
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())){
--
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