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<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 &nbsp;<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 &copy; 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>
melodicreport 0 → 100755
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#!/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
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-------------------------------------
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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