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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<title>LCModel's home page</title>
<style type="text/css">
body{
margin:10;
padding:10px 0 0 150px;
padding:0 0 0 175px;
background:#ccc;
background:#e0ffff;
}
div#left-sidebar{
position:absolute;
top:10px;
left:0;
width:175px;
background:#ccc;
background:#e0ffff;
color: #000;
}
div#content{
background:#fff;
}
@media screen{
body>div#left-sidebar{
position:fixed;
}
}
* html body{
overflow:hidden;
}
* html div#content{
height:100%;
overflow:auto;
}
</style>
</head>
<body>
<div id="left-sidebar">
<ul>
<li><a href="lcmodel.shtml">LCModel home</a></li><br>
<hr>
<li><a href="one-page.shtml">brain</a></li>
<li><a href="fig-weak-naa.shtml">brain tumor</a></li>
<li><a href="fig-strong-lipid.shtml">brain + lipids</a></li>
<li><a href="fig-lipid-1.shtml">bone</a></li>
<li><a href="fig-breast-1.shtml">breast</a></li>
<li><a href="fig-liver-1.shtml">liver</a></li>
<li><a href="fig-muscle.shtml">muscle</a></li>
<li><a href="fig-mega.shtml">MEGA-PRESS</a></li><br>
<hr>
<li><a href="lcm-test.shtml">free download</a></li>
<li><a href="lcm-license.shtml">license</a></li>
<li><a href="lcm-applications.shtml">early applications</a></li>
<li><a href="file-selector.shtml">analysis Step 1</a></li>
<li><a href="control-parameters.shtml">analysis Step 2</a></li>
<li><a href="lcm-manual.shtml">user manual</a></li>
<li><a href="asia.shtml">Japan and China</a></li>
</ul>
</div>
<div id="content">
<CENTER><H1>LCModel</H1></CENTER>
<H3>Application:</H3>
<UL>
<LI>Automatic quantification of <I>in vivo</I> proton MR spectra.</LI>
<BR>
<LI>Some very early user applications of LCModel can be seen in the
<A HREF="lcm-applications.shtml">sample publications list</A>.</LI>
</UL>
<BR>
<BR>
<H3><b><font color="#FF0000">News:</font></b></H3>
Stephen Provencher is no longer available. LCModel is now free software. You
can use it by entering (the first time only) the command:
<pre><CODE> touch $HOME/.lcmodel/license </CODE></pre>
and for each analysis the following in Figure 7.7 of the
<A HREF="lcm-manual.shtml">User's Manual</A>:
<pre><CODE> key = 210387309</CODE></pre>
Optionally, you can also enter:
<pre><CODE> owner = 'your group and laboratory name'</CODE></pre>
<BR>
Two other things you need are:
<UL>
<LI> Input data in LCModel RAW format, as specified in Chapter 5 of the
<A HREF="lcm-manual.shtml">User's Manual</A>, can also be made using tools on
the Internet or (for older data) using the recommended
LCMgui GUI decribed below.
<BR>
<BR>
<LI> Only for brain:
Basis sets of <A HREF="lcm-basis.shtml">model metabolite spectra</A>.
(See Sections 9.2 and 9.3 of the manual for other organs.)
</UL>
<BR>
<BR>
There is a <A HREF="pub/LCModel/LCModel.exe.zip">Windows version</A>, but
without the GUI; you use Chapter 5 of the <A HREF="lcm-manual.shtml">User's
Manual</A>
<BR>
<BR>
The <A HREF="pub/LCModel/source.zip">source code</A> worked with the
Intel Windows
Fortran compiler IFORT. For other compilers, you will probably have to
find a substitute for FDATE, which returns the time and date. For
Linux, there is a <A HREF="pub/LCModel/Makefile">sample
Makefile</A>.
<BR>
<BR>
<H3><b><font color="#FF0000">Please note:</font></b></H3> Much of the rest of
this website has not been updated since
LCModel became free software.
<BR>
<BR>
<H3>Download, Install & Test:</H3>
<UL>
<LI>You can freely download the complete <A
HREF="lcm-test.shtml">LCMgui/LCModel package</A> for your Linux PC. (The two
commands needed for
installation and the run with the test data are also specified.) You can also
test the preparation and input of your own data to LCModel.
</UL>
<BR>
<H3>Past News:</H3>
LCModel Version 6.3.
<UL>
<LI> Estimation of GABA with <A HREF="fig-mega.shtml">MEGA-PRESS</A>.
<BR>
<BR>
<LI> Improved estimation of weaker metabolites, especially glutamine.
<BR>
<BR>
<LI> Improved analyses of muscle, lipid, breast and liver spectra.
</UL>
<BR>
LCModel Version 6.2. While the main
application remains <A HREF="one-page.shtml">brain</A>, options have been
added for more primitive spectra:
<UL>
<LI> Mainly water & lipids, as in fat and
<A HREF="fig-lipid-1.shtml">bone</A>.
<BR>
<BR>
<LI> Water & lipids plus possibly choline, as in
<A HREF="fig-breast-1.shtml">breast</A> and
<A HREF="fig-liver-1.shtml">liver</A>.
<BR>
<BR>
<LI>LCModel Version 6.1 with new
options, including analysis of <A HREF="fig-muscle.shtml">muscle spectra</A>,
particularly for IMCL.
<BR>
<BR>
<LI>A Linux version for PCs (with Intel or AMD processors) is
now available. It is much faster than UNIX, with an excellent hardware
performance/price ratio, particularly interesting for MRSI.
<BR>
<BR>
<LI>Major new LCModel Version 6
with many new features, including:
<BR>
<BR>
<LI>Estimates of macromolecule and lipid contributions in <A
HREF="one-page.shtml">normals</A> and in pathologies (e.g., tumors) <A
HREF="fig-strong-lipid.shtml">with strong lipid</A> signals and <A
HREF="fig-weak-naa.shtml">without strong lipid</A> signals.
<BR>
<BR>
<LI>Analyses of full 2D slices or rectangular 2D subsets of 2D or 3D MRSI
data sets.
<BR>
<BR>
</UL>
<H3>Features:</H3>
<UL>
<LI>Fully automatic, non-interactive, operator-independent: time-domain
data input, <A HREF="one-page.shtml">one-page summary</A> output.
<BR>
<BR>
<LI>Fully developed, over 29 years, with spectra analyzed from a wide
variety of scanners and field strengths at more than 1000 sites.</LI>
<BR>
<BR>
</UL>
<H3>Methods are described in:</H3>
<UL>
<LI>Stephen Provencher: Estimation of metabolite concentrations from localized
<I>in vivo</I> proton NMR spectra. <I>Magn Reson Med</I>
<STRONG>30</STRONG>, 672 (1993).</LI>
<BR>
<LI><A HREF="lcm-manual.shtml">User's Manual</A> (you can always get the
latest version here).</LI>
</UL>
<BR>
<BR>
<H3>LCMgui Graphical User Interface</H3>
The normal usage is to supply the time-domain data as a simple text
file to LCModel. A possible alternative is the LCMgui graphical user
interface:
<UL>
<LI> Freely available for use with LCModel.
<BR>
<BR>
<LI>Simplified usage, often only with mouse clicks, in two steps:
<OL>
<LI> Select the data with the <A
HREF="file-selector.shtml">File Selector</A>;
<BR>
<LI> Start LCModel (optionally checking and modifying any
settings) in the <A HREF="control-parameters.shtml">Control
Window.</A></LI>
</OL>
<BR>
<LI> Currently for the following (older) single-voxel data:
<UL>
<LI>Bruker <CODE>fid</CODE> files.
<BR>
<LI>GE 5.x Probe raw P-files and spectrum G-files.
<BR>
<LI>GE Probe raw P-files.
Also for P-files with multi-channel (phased-array) data.
<BR>
<LI>Hitachi data: LCModel is
part of the Hitachi software; no need to use
LCMgui.
<BR>
<LI>Philips SDAT/SPAR pairs and enhanced DICOM files.
<BR>
<LI>Picker (later Marconi, now Philips) DUMP files.
<BR>
<LI> Siemens *rda files transferred from the syngo PC
console and
Siemens raw files from the (old) Numaris-3 Unix console.
<BR>
<LI>Toshiba rawData files and
Version 7.xx (and later) DICOM files.
<BR>
<LI>Varian/Agilent <CODE>fid</CODE> files.
<BR>
<LI>Other data types using your own conversion script.
</UL>
<BR>
<LI>Currently for the following MRSI data:
<UL>
<LI>Philips, Siemens & Toshiba single-channel data,
including interactive display, selection and analysis of full 2D slices or
rectangular subsets. (Instructions in Sections 3.2 & 3.7 of the <A
HREF="lcm-manual.shtml">LCModel Manual</A>.) <BR>
<LI>Other data types using your own conversion script;
<BR>
<LI><A NAME="sage"> </A>For GE MRSI (and single-voxel) data, Mary
McLean's SAGE/LCModel interface [MA McLean <I>et al, Magn Reson
Med</I>
<STRONG>44,</STRONG> 401 (2000)] is integrated into GE's SAGE
Research version (from SAGE Dev2002.1).
<BR>
</UL>
</UL>
<BR>
<HR>
<BR>
To <A HREF="../index.shtml">Inverse Problems home page</A> <BR>
</DIV>
</BODY>
</HTML>