From a37eae0fad437398a2b0cadcac9e644a5a1677d4 Mon Sep 17 00:00:00 2001
From: Christian Beckmann <c.beckmann@donders.ru.nl>
Date: Thu, 2 Aug 2007 16:07:39 +0000
Subject: [PATCH] MELODIC 3.04
---
meldata.cc | 12 +++++-
melodic.cc | 14 +++----
melodic.h | 2 +-
melodic.tcl | 2 +-
meloptions.h | 7 +++-
melreport.cc | 102 +++++++++++++++++++++++++++++----------------------
melreport.h | 84 ++++++++++++++++++++++++++++++++----------
7 files changed, 148 insertions(+), 75 deletions(-)
diff --git a/meldata.cc b/meldata.cc
index fb227a1..cabb707 100644
--- a/meldata.cc
+++ b/meldata.cc
@@ -156,13 +156,15 @@ namespace Melodic{
Matrix alltcs = Tmodes.at(0);
for(int ctr=1; ctr < (int)Tmodes.size();ctr++)
alltcs|=Tmodes.at(ctr);
- glmT.olsfit(alltcs,Tdes,Tcon);
+ if((alltcs.Nrows()==Tdes.Nrows())&&(Tdes.Nrows()>Tdes.Ncols()))
+ glmT.olsfit(alltcs,Tdes,Tcon);
}
if(Sdes.Storage()){
Matrix alltcs = Smodes.at(0);
for(int ctr=1; ctr < (int)Smodes.size();ctr++)
alltcs|=Smodes.at(ctr);
- glmS.olsfit(alltcs,Sdes,Scon);
+ if((alltcs.Nrows()==Sdes.Nrows())&&(Sdes.Nrows()>Sdes.Ncols()))
+ glmS.olsfit(alltcs,Sdes,Scon);
}
}
@@ -180,6 +182,12 @@ namespace Melodic{
opts.varnorm.set_T(false);
}
alldat = process_file(opts.inputfname.value().at(0), numfiles) / numfiles;
+
+ if(opts.pca_dim.value() > alldat.Nrows()-2){
+ cerr << "ERROR:: too many components selected \n\n";
+ exit(2);
+ }
+
if(opts.debug.value())
save4D(alldat,string("preproc_dat") + num2str(1));
for(int ctr = 1; ctr < numfiles; ctr++){
diff --git a/melodic.cc b/melodic.cc
index 670f4bb..4aeadd4 100644
--- a/melodic.cc
+++ b/melodic.cc
@@ -139,6 +139,13 @@ int main(int argc, char *argv[]){
Matrix pmaps;//(melodat.get_IC());
Matrix mmres;
+ if( bool(opts.genreport.value()) ){
+ report.analysistxt();
+ if(melodat.get_numfiles()>1)
+ report.Smode_rep();
+ report.PPCA_rep();
+ }
+
if(opts.perf_mm.value())
mmres = mmall(logger,opts,melodat,report,pmaps);
else{
@@ -158,13 +165,6 @@ int main(int argc, char *argv[]){
}
}
- if( bool(opts.genreport.value()) ){
- report.analysistxt();
- if(melodat.get_numfiles()>1)
- report.Smode_rep();
- report.PPCA_rep();
- }
-
message("finished!" << endl << endl);
}
else {
diff --git a/melodic.h b/melodic.h
index 0eefaff..6f5134e 100644
--- a/melodic.h
+++ b/melodic.h
@@ -40,7 +40,7 @@
namespace Melodic{
-const string version = "3.03";
+const string version = "3.04";
// The two strings below specify the title and example usage that is
// printed out as the help or usage message
diff --git a/melodic.tcl b/melodic.tcl
index 4f1582d..2eb6cca 100644
--- a/melodic.tcl
+++ b/melodic.tcl
@@ -336,7 +336,7 @@ button $w.btns.load -command "feat_file:setup_dialog $w a a a [namespace current
button $w.btns.cancel -command "destroy $w" -text "Exit"
-button $w.btns.help -command "FmribWebHelp file: ${FSLDIR}/doc/melodic3/index.html" -text "Help"
+button $w.btns.help -command "FmribWebHelp file: ${FSLDIR}/doc/melodic/index.html" -text "Help"
#{{{ Utils
diff --git a/meloptions.h b/meloptions.h
index 6ffd12e..9270400 100644
--- a/meloptions.h
+++ b/meloptions.h
@@ -77,6 +77,7 @@ class MelodicOptions {
Option<string> filter;
Option<bool> genreport;
+ Option<string> guireport;
Option<string> bgimage;
Option<float> tr;
Option<bool> logPower;
@@ -218,7 +219,7 @@ class MelodicOptions {
rank1interval(string("--rank1interval"), 10,
string("number of iterations between rank-1 approximation (TICA)\n"),
false, requires_argument,false),
- mmthresh(string("--mmthresh"), string("0.5"),
+ mmthresh(string("--mmthresh"), string("0.5"),
string("threshold for Mixture Model based inference"),
false, requires_argument),
perf_mm(string("--no_mm"), true,
@@ -239,6 +240,9 @@ class MelodicOptions {
genreport(string("--report"), false,
string("generate Melodic web report"),
false, no_argument),
+ guireport(string("--guireport"), string(""),
+ string("modify report for GUI use"),
+ false, requires_argument, false),
bgimage(string("--bgimage"), string(""),
string("specify background image for report (default: mean image)\n "),
false, requires_argument),
@@ -374,6 +378,7 @@ class MelodicOptions {
options.add(smodename);
options.add(filter);
options.add(genreport);
+ options.add(guireport);
options.add(bgimage);
options.add(tr);
options.add(logPower);
diff --git a/melreport.cc b/melreport.cc
index 01cf3aa..63e4491 100644
--- a/melreport.cc
+++ b/melreport.cc
@@ -24,24 +24,29 @@ namespace Melodic{
IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
{//start IC page
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+ (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
+ <<"px width=100% src=nav.html frameborder=0></IFRAME><BR>"<< endl
+ << "<Center>" << endl;
if(cnum>1)
IChtml << "<a href=\"" << string("IC_")+num2str(cnum-1)
- <<".html\">previous</a> - ";
- IChtml << "<a href=\"00index.html\"> index </a>" ;
+ <<".html\"><</a> - ";
+ else
+ IChtml << "<a href=\"" << string("IC_")+num2str(melodat.get_mix().Ncols())
+ <<".html\"><</a> - ";
if(cnum<dim)
- IChtml << " - <a href=\"" << string("IC_")+num2str(cnum+1)
- <<".html\">next</a><p>";
-
- IChtml << "<hr><p>" << endl;
+ IChtml << "<a href=\"" << string("IC_")+num2str(cnum+1)
+ <<".html\">></a>";
+ else
+ IChtml << "<a href=\"" << string("IC_")+num2str(1)
+ <<".html\">></a>";
+ IChtml << "<p><H3>MELODIC Component " << num2str(cnum)
+ << "<br></b></H3><hr><p>" << endl;
}
{//output IC stats
if(ICstats.Storage()>0&&ICstats.Nrows()>=cnum){
@@ -110,7 +115,8 @@ namespace Melodic{
Matrix tmptc = melodat.get_Tmodes(cnum-1).t();
//add GLM OLS fit
- if(melodat.Tdes.Storage() > 0){
+ if(melodat.Tdes.Storage()>0 &&
+ melodat.glmT.get_beta().Nrows() == melodat.Tdes.Ncols()){
tmptc &= melodat.glmT.get_beta().Column(cnum).t() * melodat.Tdes.t();
newplot.add_label(string("IC ")+num2str(cnum)+" time course");
newplot.add_label("full model fit");
@@ -182,7 +188,8 @@ namespace Melodic{
+string("f")+num2str(cnum)+".png\"></A><p>" << endl;
}//frequency plot
{//add T-mode GLM F-stats for full model fit & contrasts
- if(melodat.Tdes.Storage() > 0){
+ if(melodat.Tdes.Storage() > 0 &&
+ melodat.glmT.get_beta().Nrows() == melodat.Tdes.Ncols()){
IChtml << " <TABLE border=1 bgcolor=ffffff cellpadding=5>" <<
"<CAPTION><EM> <b>GLM (OLS) on time series </b></EM></CAPTION>" << endl
<< "<TR valign=middle><TH ><EM>GLM β's</EM> <TH> <EM> F-test on <br> full model fit </em>";
@@ -205,8 +212,8 @@ namespace Melodic{
IChtml << fixed << setprecision(5) << " p < " <<
melodat.glmT.get_pf_fmf().Column(cnum) <<
"<BR> (uncorrected for #comp.)</TD>" << endl;
- }
- if(melodat.Tcon.Storage() > 0){
+ if(melodat.Tcon.Storage() > 0 &&
+ melodat.Tdes.Ncols() == melodat.Tcon.Nrows()){
IChtml << fixed << setprecision(2) << "<TD><TABLE border=0><TR><TD align=right>" <<endl;
for(int ctr=1; ctr <= melodat.Tcon.Nrows() ; ctr++)
IChtml << "COPE(" << num2str(ctr) << "): <br>" << endl;
@@ -225,7 +232,8 @@ namespace Melodic{
IChtml << fixed << setprecision(5) <<" p < " << melodat.glmT.get_p().Column(cnum).Row(ctr) <<
"<BR>" << endl;
IChtml << "</TABLE></td></tr>" << endl;
- }
+ }
+ }
IChtml << "</TABLE><p>" << endl;
}
@@ -240,7 +248,8 @@ namespace Melodic{
//add GLM OLS fit
//newplot.setscatter(smode,2);
- if(melodat.Sdes.Storage() > 0){
+ if(melodat.Sdes.Storage() > 0&&
+ melodat.glmS.get_beta().Nrows() == melodat.Sdes.Ncols()){
smode |= melodat.Sdes * melodat.glmS.get_beta().Column(cnum);
newplot.add_label(string("IC ")+num2str(cnum)+" subject/session-mode");
newplot.add_label("full model fit");
@@ -272,7 +281,8 @@ namespace Melodic{
+string("b")+num2str(cnum)+".png\"></A><p>" << endl;
}
{//add S-mode GLM F-stats for full model fit & contrasts
- if(melodat.Sdes.Storage() > 0){
+ if(melodat.Sdes.Storage() > 0 &&
+ melodat.glmS.get_beta().Nrows() == melodat.Sdes.Ncols()){
IChtml << " <TABLE border=1 bgcolor=ffffff cellpadding=5>" <<
"<CAPTION><EM> <b>GLM (OLS) on subject/session-mode </b></EM></CAPTION>" << endl
<< "<TR valign=middle><TH ><EM>GLM β's</EM> <TH> <EM> F-test on <br> full model fit </em>";
@@ -295,8 +305,8 @@ namespace Melodic{
IChtml << fixed << setprecision(5) << " p < " <<
melodat.glmS.get_pf_fmf().Column(cnum) <<
"<BR> (uncorrected for #comp.)</TD>" << endl;
- }
- if(melodat.Scon.Storage() > 0){
+ if(melodat.Scon.Storage() > 0 && melodat.Sdes.Storage() > 0 &&
+ melodat.Sdes.Ncols() == melodat.Scon.Nrows()){
IChtml << fixed << setprecision(2) << "<TD><TABLE border=0><TR><TD align=right>" <<endl;
for(int ctr=1; ctr <= melodat.Scon.Nrows() ; ctr++)
IChtml << "COPE(" << num2str(ctr) << "): <br>" << endl;
@@ -316,8 +326,8 @@ namespace Melodic{
"<BR>" << endl;
IChtml << "</TABLE></td></tr>" << endl;
}
+ }
IChtml << "</TABLE><p>" << endl;
-
}
}//subject mode plot
@@ -382,7 +392,7 @@ namespace Melodic{
IChtml<< "<HR><FONT SIZE=1>This page produced automatically by "
<< "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
<< version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
- << "FMRIB Software Library</A>.</FONT>" << endl
+ << "FMRIB Software Library</A>.</FONT></Center>" << endl
<< "</BODY></HTML>" << endl;
} //finish IC page
IC_rep_det(mmodel, cnum, dim);
@@ -394,24 +404,30 @@ namespace Melodic{
{//start IC2 page
IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
- IChtml2 << "<HTML> " << endl
- << "<TITLE>Component " << num2str(cnum)
- << " Mixture Model fit </TITLE>" << endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Component " << num2str(cnum)
- << " Mixture Model fit </H1>"<< endl;
-
+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+ (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
+ <<"px width=100% src=nav.html frameborder=0></IFRAME><p>"<< endl
+ << "<CENTER>";
if(cnum>1)
- IChtml2 << "<a href=\"" << string("IC_")+num2str(cnum-1)
- <<"_MM.html\">previous</a> - ";
- IChtml2 << "<a href=\""+ mmodel.get_prefix() +
- ".html\"> up to IC report </a>";
+ IChtml2 << "<b><a href=\"" << string("IC_")+num2str(cnum-1)
+ <<"_MM.html\"><</a> - ";
+ else
+ IChtml2 << "<b><a href=\"" << string("IC_")+num2str(melodat.get_mix().Ncols())
+ <<"_MM.html\"><</a> - ";
+ // IChtml << "<a href=\"00index.html\"> index </a>" ;
+
if(cnum<dim)
- IChtml2 << " - <a href=\"" << string("IC_")+num2str(cnum+1)
- <<"_MM.html\">next</a><p>";
- IChtml2 << "<hr><p>" << endl;
- }
+ IChtml2 << "<a href=\"" << string("IC_")+num2str(cnum+1)
+ <<"_MM.html\">></a>";
+ else
+ IChtml2 << "<a href=\"" << string("IC_")+num2str(1)
+ <<"_MM.html\">></a>";
+ IChtml2 << "<p><H3>Component " << num2str(cnum)
+ << " Mixture Model fit <br></b></H3><hr><p>" << endl;
+ }
volume4D<float> tempVol;
@@ -554,7 +570,7 @@ namespace Melodic{
IChtml2<< "<HR><FONT SIZE=1>This page produced automatically by "
<< "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
<< version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
- << "FMRIB Software Library</A>.</FONT>" << endl
+ << "FMRIB Software Library</A>.</FONT></CENTER>" << endl
<< "</BODY></HTML>" << endl;
} //finish IC2 page
}
@@ -706,7 +722,7 @@ namespace Melodic{
void MelodicReport::PPCA_rep(){
{//plot time course
- report << "<p> <H3>PCA estimates </H3> <p>" << endl;
+ report << "<p><hr><b>PCA estimates </b> <br>" << endl;
Matrix what;
miscplot newplot;
@@ -737,7 +753,7 @@ namespace Melodic{
}
void MelodicReport::Smode_rep(){
- report << "<p> <H3>TICA Subject/Session modes </H3> <p>" << endl;
+ report << "<b>TICA Subject/Session modes </b> <p>" << endl;
miscplot newplot;
Matrix allmodes = melodat.get_Smodes().at(0);
for(int ctr = 1; ctr < (int)melodat.get_Smodes().size();++ctr)
diff --git a/melreport.h b/melreport.h
index 93cd08e..3989f8a 100644
--- a/melreport.h
+++ b/melreport.h
@@ -44,35 +44,75 @@ namespace Melodic{
const time_t tmptime = time(NULL);
report.makeDir(logger.appendDir("report"),"00index.html");
- report << "<HTML>" << endl << endl
- << "<TITLE>MELODIC Report</TITLE>"<< endl <<endl
- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
- << "/doc/images/fsl-bg.jpg\">" << endl
- << endl << "<hr><CENTER> " << endl
- << "<H1>MELODIC Report</H1>"
- << endl
- << report.getDir() << "/" << report.getLogFileName()
- << "<br>" << endl
- << ctime(&tmptime) << "<br>" << endl;
- report << "</CENTER>" << endl << endl
- << "<hr><H2>Components:</H2> <p>" << endl << endl;
+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+ (string) getenv("FSLDIR") +"/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ loghtml.setDir(report.getDir(),"log.html");
+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+ (string) getenv("FSLDIR") +"/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ navigator.setDir(report.getDir(),"nav.html");
+ head.setDir(report.getDir(),"head.html");
+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
+ (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+ head << "<link REL=stylesheet TYPE=text/css href=file:"+
+ (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+ head <<"<TABLE BORDER=0><TR>" << endl
+ <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
+ <<"<TABLE BORDER=0>"<< endl
+ <<"<tr><td align=center><font size=+3><b>MELODIC Report</b>"<< endl
+ <<"</font><tr><td valign=center align=center> <p>"<< endl
+ << report.getDir() << "/" << report.getLogFileName() << "<br>"
+ << ctime(&tmptime) << "</tr>"<< endl
+ <<"<tr valign=bottom><td align=center>"<< endl
+ << "</tr></table>" << endl
+ << "<TD ALIGN=RIGHT>" << endl
+ << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
+ << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
+ << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
+ if(opts.guireport.value()==""){
+ report <<"<OBJECT data=head.html></OBJECT>" << endl;
+ loghtml <<"<OBJECT data=head.html></OBJECT>" << endl;
+ }else{
+ report <<"<OBJECT data="<<opts.guireport.value()<< "></OBJECT>"<< endl;
+ loghtml <<"<OBJECT data="<<opts.guireport.value()<< "></OBJECT>"<< endl;
+ }
+ report << "<IFRAME height=100px width=100% src=nav.html frameborder=0></IFRAME><p>"<< endl;
+ loghtml << "<IFRAME height=100px width=100% src=nav.html frameborder=0></IFRAME><p>"
+ <<"<pre>../melodic.log</pre>" <<endl;
+ navigator <<"<CENTER><TABLE BORDER=0><TR>" << endl
+ <<"<TD ALIGN=CENTER WIDTH=100%><FONT SIZE=-1>"<<endl
+ <<"<A HREF=\"00index.html\" target=\"_top\">Main</A> - ";
+ // if(opts.guireport.value()=="")
+ // navigator << "<A HREF=\"log.html\" target=\"_top\">Log</A> - ";
+ navigator <<"Components: ";
+ navigator.flush();
}
}
~MelodicReport(){
if( bool(opts.genreport.value()) ){
- report << "<HR><FONT SIZE=1>This page produced automatically by "
- << "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
- << version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
- << "FMRIB Software Library</A>.</FONT>" << endl
- << "</BODY></HTML>" << endl;
+ report << "<HR><CENTER><FONT SIZE=1>This page produced automatically by "
+ << "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
+ << version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
+ << "FMRIB Software Library</A>.</FONT></CENTER>" << endl
+ << "</BODY></HTML>" <<endl;
+ loghtml << "<HR><CENTER><FONT SIZE=1>This page produced automatically by "
+ << "<A HREF=\"http://www.fmrib.ox.ac.uk/fsl/melodic/index.html\"> MELODIC</A> Version "
+ << version << " - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - "
+ << "FMRIB Software Library</A>.</FONT></CENTER>" << endl
+ << "</BODY></HTML>" <<endl;
+ navigator << "</FONT></TD>"<<endl<<"</TR></TABLE></CENTER><hr>" <<endl;
}
}
inline void analysistxt(){
if( bool(opts.genreport.value()) ){
- report << "<hr><h2>Analysis methods</h2> <p>"<<endl;
+ report << "<b>Analysis methods</b> <br>"<<endl;
report << "Analysis was carried out using MELODIC (Multivariate Exploratory Linear Decomposition into Independent Components) Version "<< version <<", 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;
@@ -122,7 +162,7 @@ namespace Melodic{
inline void refstxt(){
if( bool(opts.genreport.value()) ){
- report << "<h3>References</h3> <p>"<<endl;
+ report << "<b>References</b> <br>"<<endl;
report << "[Hyvärinen 1999] A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis. IEEE Transactions on Neural Networks 10(3):626-634, 1999.<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;
@@ -163,7 +203,8 @@ namespace Melodic{
inline void addlink(string where, string what){
if( bool(opts.genreport.value()) ){
- report << "<A HREF=\"" << where << "\"> " << what << "</A> ";
+ navigator << "<A HREF=\"" << where << " \"target=\"_top\"> " << what << "</A> ";
+ navigator.flush();
}
}
@@ -193,6 +234,9 @@ namespace Melodic{
MelodicOptions &opts;
Log &logger;
Log report;
+ Log navigator;
+ Log head;
+ Log loghtml;
Log IChtml;
Log IChtml2;
--
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