From 7d4aa0417a4cda59923605bed100636dd283dc1c Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Fri, 21 Feb 2003 16:48:47 +0000
Subject: [PATCH] Initial revision
---
doc/index.html | 100 ++++++++++++++++++++++++++++++++++++
melodicreport | 135 +++++++++++++++++++++++++++++++++++++++++++++++++
out.txt | 135 +++++++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 370 insertions(+)
create mode 100644 doc/index.html
create mode 100755 melodicreport
create mode 100644 out.txt
diff --git a/doc/index.html b/doc/index.html
new file mode 100644
index 0000000..4899123
--- /dev/null
+++ b/doc/index.html
@@ -0,0 +1,100 @@
+<HTML><HEAD><TITLE>MELODIC</TITLE>
+</HEAD><BODY BACKGROUND="../images/fsl-bg.jpg">
+<hr><TABLE BORDER=0 WIDTH="100%"><TR>
+<TD ALIGN=CENTER><H1>MELODIC - User Guide</H1>
+(Multivariate Exploratory Linear Optimized Decomposition into Independent Components)<br>
+ICA-Based Model-Free Analysis of 4D Data<br>
+MELODIC Version 2.0
+<TD ALIGN=RIGHT><a href="../index.html"><IMG BORDER=0 SRC="../images/fsl-logo.jpg"></a>
+</TR></TABLE>
+
+<HR><H2>INTRODUCTION</H2>
+
+<P>MELODIC (Multivariate Exploratory Linear Optimized Decomposition
+into Independent Components) uses ICA (Independent Component Analysis)
+to decompose 4D data (for example FMRI data) into different
+interesting spatial and temporal components. It can pick out different
+activation and artefactual components without any model being
+specified. Thus the output is a new 4D data set (each volume being a
+separate spatial component) and a text file of separate time courses
+(temporal components).
+
+<P>For more detail on MELODIC and an updated journal reference, see
+the <A
+HREF="http://www.fmrib.ox.ac.uk/analysis/research/melodic/">MELODIC
+research web page</A>. If you use MELODIC in your research, please
+quote the journal reference listed there.
+
+<p>The different MELODIC programs are:
+<UL>
+<LI><a href="#Melodic">Melodic</a> - MELODIC GUI<br>
+<LI><a href="#melodic">melodic</a> - command-line MELODIC program<br>
+</UL>
+
+<A NAME="Melodic"></A><hr><H2>Melodic GUI</H2>
+
+<center><IMG SRC="./mel1.png" ALIGN=CENTER></center>
+
+<p>Press <code>Select 4D data</code> and select the input data.
+
+<p><center><IMG SRC="./mel2.png" ALIGN=CENTER></center>
+
+<p>Low-frequency drifts and motion in the data can adversely affect
+the decomposition. In most cases, you would want to motion-correct the
+data and remove these drifts first. This can be done from within the
+Melodic GUI <code>Pre-stats</code> section.
+
+<center><IMG SRC="./mel3.png" ALIGN=CENTER></center>
+
+The MELODIC section finally lets you control some of the options for
+ the decomposition.
+The default setting will most probably already be set to what you
+ would want most of the time.
+
+<p> By default, Melodic will automatically estimate the number of
+ components from the data - you can switch this
+ option off and then can specify the number of
+ components explicitly.<p>
+Melodic will also by default carry out inference on the estimated maps
+ using the mixture model approach. A threshold level of 0.5
+ in the case of alternative hypothesis testing means that a
+ voxel 'survives' thresholding as soon as the probability
+ of being in the 'active' class (as modelled by the Gamma
+ densities) exceeds the probability of being in the
+ 'background' noise class. This threshold level assumes that
+ you are placing an equal loss on false-positives and
+ false-negatives. If, however, you consider e.g. false-positives as
+ being twice as bad as false-negatives you should change this value
+ to 0.66...<p>
+Now simply press <code>Go</code><p>
+
+Melodic will then generate the results and
+your terminal window will tell you where to find the web report.
+
+
+
+Each webpage shows one spatial map thresholded and rendered on top of an example functional scan
+followed by the relevant time-course of the ICA decomposition and the
+ power-spectrum of the time-course. If you click on the
+ thresholded map, you can inspect the raw IC output
+ together with probability maps and the Mixture Model
+ fit. Use <code>previous</code> and <code>next</code> to
+ view another component map.<p>
+
+<A NAME="melodic"></A><HR><H2>melodic COMMAND-LINE PROGRAM</H2>
+
+<p>Type <b>melodic --help</b> to get usage.
+
+
+<p><HR><FONT SIZE=1>Copyright © 2001-2002, University of
+Oxford. Written by C. Beckmann and <A
+HREF="http://www.fmrib.ox.ac.uk/~steve/index.html">S. Smith</A>.</FONT>
+
+<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+
+</BODY></HTML>
+
+
diff --git a/melodicreport b/melodicreport
new file mode 100755
index 0000000..6d6b585
--- /dev/null
+++ b/melodicreport
@@ -0,0 +1,135 @@
+#!/bin/sh
+
+# the next line restarts using wish \
+exec $FSLDIR/bin/tclsh "$0" "$@"
+
+if { [ lindex $argv 0 ] == "" } {
+ puts "Usage: melodicreport <melodic_output_directory> \[background_image \]"
+ exit
+}
+
+set background 0
+if { [ lindex $argv 1 ] != "" } {
+ set background 1
+ set bgimage [ lindex $argv 1 ]
+}
+
+set S 0.2
+catch { [ expr $S ] } errrr
+
+set FSLDIR $env(FSLDIR)
+
+set MD [ lindex $argv 0 ]
+catch { exec sh -c "mkdir ${MD}/report" }
+
+if { ! [ file exists ${MD}/melodic_IC.hdr ] || ! [ file exists ${MD}/melodic_IC.img ] } {
+ puts "No MELODIC output melodic_IC.hdr/.img - exiting."
+ exit
+}
+
+set REPORTFILE ${MD}/report/report.html
+set report [ open $REPORTFILE "w" ]
+fconfigure $report -buffering none
+
+puts $report "<HTML>
+
+<TITLE>MELODIC Report</TITLE>
+
+<BODY BACKGROUND=\"file:${FSLDIR}/doc/images/fsl-bg.jpg\">
+
+<hr><CENTER>
+<H1>MELODIC Report</H1>
+$REPORTFILE<br>
+[ exec date ]
+</CENTER>
+
+<hr><H2>Components:</H2><p>"
+
+set dim [ exec sh -c "${FSLDIR}/bin/avwval ${MD}/melodic_IC dim4" ]
+set npts [ expr [ exec sh -c "cat ${MD}/melodic_mix | wc -l" ] * 1 ]
+set xscale [ expr $npts * 4 ]
+if { $xscale < 750 } {
+ set xscale 750
+}
+if { $xscale > 3000 } {
+ set xscale 3000
+}
+set xscale [ expr $xscale / 750.0 ]
+
+for { set i 1 } { $i <= $dim } { incr i 1 } {
+
+ puts $report "<a href=\"c${i}.html\">$i</a>"
+
+ exec sh -c "${FSLDIR}/bin/avwroi ${MD}/melodic_IC ${MD}/grot [ expr $i - 1 ] 1"
+ catch { exec sh -c "${FSLDIR}/bin/avwstats ${MD}/grot -R" } minmax
+ set absmin [ expr abs ( [ lindex $minmax 0 ] ) ]
+ set absmax [ expr abs ( [ lindex $minmax 1 ] ) ]
+ if { $absmin > $absmax } {
+ set absmax $absmin
+ }
+ set absmax [ expr $absmax * 0.75 ]
+
+ if { $background == 0 } {
+ exec sh -c "${FSLDIR}/bin/slicer ${MD}/grot -l ${FSLDIR}/etc/luts/render3.lut -s 2 -i -$absmax $absmax -A 950 ${MD}/grot.ppm"
+ } else {
+ set llimit [ expr $absmax / 6.0 ]
+ exec sh -c "${FSLDIR}/bin/avwmaths ${MD}/grot -mul -1 ${MD}/grotinv"
+ exec sh -c "${FSLDIR}/bin/overlay 1 0 $bgimage -a ${MD}/grot $llimit $absmax ${MD}/grotinv $llimit $absmax ${MD}/grotoverlay"
+ exec sh -c "${FSLDIR}/bin/slicer ${MD}/grotoverlay -s 2 -A 950 ${MD}/grot.ppm"
+ }
+
+ exec sh -c "${FSLDIR}/bin/convert ${MD}/grot.ppm ${MD}/report/s$i.gif"
+
+ exec sh -c "cat ${MD}/melodic_mix | awk '{ print \$$i }' > ${MD}/report/t${i}.txt"
+ exec sh -c "echo \"set term pbm color ; set size $xscale,0.25 ; set title 'Timecourse (TRs)' ; plot '${MD}/report/t${i}.txt' title '' with lines\" | ${FSLDIR}/bin/gnuplot > ${MD}/grot.ppm"
+ exec sh -c "${FSLDIR}/bin/convert ${MD}/grot.ppm ${MD}/report/t$i.gif"
+
+ exec sh -c "cat ${MD}/melodic_FTmix | awk '{ print NR \" \" \$$i }' > ${MD}/report/f${i}.txt"
+ exec sh -c "echo \"set term pbm color ; set size $xscale,0.25 ; set title 'FT of Timecourse (cycles) frequency(Hz)=cycles/($npts*TR) period(s)=($npts*TR)/cycles' ; plot '${MD}/report/f${i}.txt' title '' with lines\" | ${FSLDIR}/bin/gnuplot > ${MD}/grot.ppm"
+ exec sh -c "${FSLDIR}/bin/convert ${MD}/grot.ppm ${MD}/report/f$i.gif"
+
+ set creport [ open ${MD}/report/c${i}.html "w" ]
+
+ puts $creport "<HTML>
+ <TITLE>MELODIC Component $i</TITLE>
+ <BODY BACKGROUND=\"file:${FSLDIR}/doc/images/fsl-bg.jpg\">
+ <hr><CENTER><H1>MELODIC Component $i</H1>
+ "
+
+ if { $i > 1 } {
+ puts $creport "<a href=\"c[ expr $i - 1 ].html\">previous</a> - "
+ }
+
+ puts $creport "<a href=\"report.html\">index</a>"
+
+ if { $i < $dim } {
+ puts $creport " - <a href=\"c[ expr $i + 1 ].html\">next</a>"
+ }
+
+ puts $creport "
+ <hr><p>
+
+ <IMG BORDER=0 SRC=\"s$i.gif\"><p>
+ <a href=\"t$i.txt\"><IMG BORDER=0 SRC=\"t$i.gif\"></a><p>
+ <a href=\"f$i.txt\"><IMG BORDER=0 SRC=\"f$i.gif\"></a><p>
+
+ <hr></CENTER></BODY></HTML>
+ "
+ close $creport
+}
+
+exec sh -c "/bin/rm -f ${MD}/grot*"
+
+puts $report "<HR><FONT SIZE=1>This page produced automatically by MELODIC - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - FMRIB's Software Library</A>.</FONT>
+
+</BODY></HTML>
+"
+
+close $report
+
+puts "Finished melodicreport at [ exec date ]
+To view the MELODIC report point your web browser at
+$REPORTFILE
+"
+
+exit
diff --git a/out.txt b/out.txt
new file mode 100644
index 0000000..02559be
--- /dev/null
+++ b/out.txt
@@ -0,0 +1,135 @@
+-------------------------------------
+meldata.h
+-------------------------------------
+
+
+53,55d112
+<
+< inline Matrix& get_pcaEVN() {return pcaEVN;}
+< inline void set_pcaEVN(Matrix& Arg) {pcaEVN = Arg;}
+59,61c116,118
+<
+< inline DiagonalMatrix& get_pcaDVN() {return pcaDVN;}
+< inline void set_pcaDVN(DiagonalMatrix& Arg) {pcaDVN = Arg;}
+---
+>
+> inline Matrix& get_data() {return Data;}
+> inline void set_data(Matrix& Arg) {Data = Arg;}
+96,100c153,154
+< // inline Matrix& get_DataVN() {
+< // Matrix tmp;
+< // tmp = SP(Data,ones(Data.Nrows(),1)*stdDevi);
+< // return tmp;
+< // }
+---
+> inline Matrix& get_DataVN() {return DataVN;}
+> inline void set_DataVN(Matrix& Arg) {DataVN = Arg;}
+123,131d176
+< inline void calc_Corr() { Corr = cov(Data.t());}
+< inline void calc_CorrVN() {
+< CorrVN = cov(SP(Data,ones(Data.Nrows(),1)*stdDevi).t());
+< }
+<
+< inline SymmetricMatrix& get_Corr() {return Corr;}
+< inline SymmetricMatrix& get_CorrVN() {return CorrVN;}
+<
+<
+157,162d201
+< Matrix pcaEVN;
+< DiagonalMatrix pcaDVN;
+<
+< SymmetricMatrix Corr;
+< SymmetricMatrix CorrVN;
+<
+178a218
+> Matrix DataVN;
+
+
+-------------------------------------
+meldata.cc
+-------------------------------------
+
+
+103d162
+<
+107,108c166,167
+< //Corr = cov(Data.t());
+< calc_Corr();
+---
+> SymmetricMatrix Corr;
+> Corr = cov(Data.t());
+128c187
+<
+---
+>
+132,145c191,192
+<
+< if(opts.segment.value().length()>0){
+< Matrix Res;
+< Res = ones(Data.Nrows(),1)*RXweight;
+< if(opts.varnorm.value()){
+< Res = SP(SP(Data,ones(Data.Nrows(),1)*stdDevi),Res);
+< }
+< else
+< Res = SP(Data,Res);
+< Data = Res;
+< }
+<
+< calc_CorrVN();
+<
+---
+>
+> DataVN = SP(Data,ones(Data.Nrows(),1)*stdDevi);
+147,148c194
+< Data = SP(Data,ones(Data.Nrows(),1)*stdDevi);
+< Corr = CorrVN;
+---
+> Data = DataVN;
+151,153d196
+< else
+< calc_Corr();
+<
+
+-------------------------------------
+melodic.cc
+-------------------------------------
+
+92c152
+< pcaobj.perf_pca(melodat.get_Data());
+---
+> pcaobj.perf_pca(melodat.get_DataVN());
+
+-------------------------------------
+melpca.cc
+-------------------------------------
+
+
+30a91,92
+> SymmetricMatrix Corr;
+>
+34,38c96,99
+< if(opts.varnorm.value()){
+< Res = SP(SP(melodat.get_Data(),ones(melodat.get_Data().Nrows(),1)*melodat.get_stdDevi()),Res);
+< }
+< else
+< Res = SP(melodat.get_Data(),Res);
+---
+> Res = SP(melodat.get_DataVN(),Res);
+> melodat.set_DataVN(Res);
+> Res = ones(Data.Nrows(),1)*melodat.get_RXweight();
+> Res = SP(melodat.get_Data(),Res);
+40,41d100
+< melodat.calc_Corr();
+< melodat.calc_CorrVN();
+43a103,104
+> Corr = cov(melodat.get_Data().t());
+>
+47c108
+< EigenValues(melodat.get_Corr(),tmpD,tmpE);
+---
+> EigenValues(Corr,tmpD,tmpE);
+170c231
+< Corr = cov(SP(melodat.get_Data(),ones(melodat.get_Data().Nrows(),1)*melodat.get_stdDevi()).t());
+---
+> Corr = cov(melodat.get_DataVN().t());
+
--
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