Skip to content
Snippets Groups Projects
Commit 7f2973a5 authored by Christian Beckmann's avatar Christian Beckmann
Browse files

ready for fsl 3.2

parent f7614910
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
meldata.cc
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melgmix.h
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melica.h
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melodic.cc
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2003 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melodic.h
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
meloptions.cc
+ 1
− 1
View file @ 7f2973a5
......@@ -6,7 +6,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
meloptions.h
+ 1
− 1
View file @ 7f2973a5
......@@ -6,7 +6,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melpca.cc
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-200 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melpca.h
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melreport.cc
+ 1
− 1
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......
melreport.h
+ 7
− 7
View file @ 7f2973a5
......@@ -5,7 +5,7 @@
Christian F. Beckmann, FMRIB Image Analysis Group
Copyright (C) 1999-2002 University of Oxford */
Copyright (C) 1999-2004 University of Oxford */
/* CCOPYRIGHT */
......@@ -84,7 +84,7 @@ namespace Melodic{
if( bool(opts.genreport.value()) ){
report << "<hr><h2>Analysis methods</h2> <p>"<<endl;
report << "Analysis was carried out using MELODIC (Multivariate Exploratory Linear Decomposition into Independent Components) Version 2.00, part of FSL (FMRIB's Software Library, <A HREF=\"http://www.fmrib.ox.ac.uk/fsl/\">www.fmrib.ox.ac.uk/fsl</A>), an implementation for the estimation of a Probabilistic Independent Component Analysis model [Beckmann 2002]."<<endl;
report << "Analysis was carried out using MELODIC (Multivariate Exploratory Linear Decomposition into Independent Components) Version 2.00, part of FSL (FMRIB's Software Library, <A HREF=\"http://www.fmrib.ox.ac.uk/fsl/\">www.fmrib.ox.ac.uk/fsl</A>), an implementation for the estimation of a Probabilistic Independent Component Analysis model [Beckmann 2004]."<<endl;
report << "The following melodic pre-processing was applied to the input data file: "<< endl;
......@@ -103,7 +103,7 @@ namespace Melodic{
if(melodat.get_PPCA().Storage()>0){
report << "probabilistic Principal Component Analysis where the number of dimensions was estimated using ";
if(opts.pca_est.value() == string("lap"))
report << "the Laplace approximation to the Bayesian evidence of the model order [Beckmann 2001, Minka 2000]. " << endl;
report << "the Laplace approximation to the Bayesian evidence of the model order [Minka 2000, Beckmann 2004]. " << endl;
else
if(opts.pca_est.value() == string("bic"))
report << "the <em> Bayesian Information Criterion</em> (BIC) [Kass 1993]. " << endl;
......@@ -114,7 +114,7 @@ namespace Melodic{
if(opts.pca_est.value() == string("aic"))
report << "the <em> Akaike Information Criterion</em> (AIC) [Akaike 1969]. " << endl;
else
report << "a committee of approximations to Bayesian the model order [Beckmann 2001, Minka 2000]. " << endl;
report << "a committee of approximations to Bayesian the model order [Beckmann 2004]. " << endl;
}
else
......@@ -126,7 +126,7 @@ namespace Melodic{
report << "Estimated Component maps were divided by the standard deviation of the residual noise";
if(opts.perf_mm.value())
report << " and thresholded by fitting a mixture model to the histogram of intensity values [Beckmann 2002]. <p>" << endl;
report << " and thresholded by fitting a mixture model to the histogram of intensity values [Beckmann 2004]. <p>" << endl;
else
report <<".<p>" << endl;
......@@ -140,7 +140,7 @@ namespace Melodic{
report << "<h3>References</h3> <p>"<<endl;
report << "[Hyv&auml;rinen 1999] A. Hyv&auml;rinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis. IEEE Transactions on Neural Networks 10(3):626-634, 1999.<br> " << endl;
report << "[Beckmann 2002] C.F. Beckmann and S.M. Smith. Probabilistic Independent Component Analysis for FMRI. <A HREF=\"http://www.fmrib.ox.ac.uk/analysis/techrep/\">Technical Report TR02CB1</A>, FMRIB Analysis Group, 2002. <br>" << endl;
report << "[Beckmann 2004] C.F. Beckmann and S.M. Smith. Probabilistic Independent Component Analysis for Functional Magnetic Resonance Imaging. IEEE Transactions on Medical Imaging 23(2):137-152 2004. <br>" << endl;
/* if(opts.perf_mm.value()){ */
/* report << "[Bullmore 1996] E. Bullmore <em>et. al.</em> Statistical methods of estimation and inference for functional MR image analysis. Magnetic Resonance in Medicine, 35(2):261-177, 1996. <br>" << endl; */
......@@ -150,7 +150,7 @@ namespace Melodic{
if(melodat.get_PPCA().Storage()>0){
report << "[Everson 2000] R. Everson and S. Roberts. Inferring the eigenvalues of covariance matrices from limited, noisy data. IEEE Trans Signal Processing, 48(7):2083-2091, 2000<br>"<<endl;
report << "[Tipping 1999] M.E. Tipping and C.M.Bishop. Probabilistic Principal component analysis. J Royal Statistical Society B, 61(3), 1999. <br>" << endl;
report << "[Beckmann 2001] C.F. Beckmann, J.A. Noble and S.M. Smith. Investigating the intrinsic dimensionality of FMRI data for ICA. In Seventh Int. Conf. on Functional Mapping of the Human Brain, 2001. <br>" << endl;
/* report << "[Beckmann 2001] C.F. Beckmann, J.A. Noble and S.M. Smith. Investigating the intrinsic dimensionality of FMRI data for ICA. In Seventh Int. Conf. on Functional Mapping of the Human Brain, 2001. <br>" << endl;*/
if(opts.pca_est.value() == string("lap"))
report << "[Minka 2000] T. Minka. Automatic choice of dimensionality for PCA. Technical Report 514, MIT Media Lab Vision and Modeling Group, 2000. <BR>"<< endl;
else
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment