LCModel

Application:

Automatic quantification of in vivo proton MR spectra.

Some very early user applications of LCModel can be seen in the sample publications list.

News:

Stephen Provencher is no longer available. LCModel is now free software. You can use it by entering (the first time only) the command:

  touch  $HOME/.lcmodel/license

and for each analysis the following in Figure 7.7 of the User's Manual:

  key = 210387309

Optionally, you can also enter:

  owner = 'your group and laboratory name'

Two other things you need are:

Input data in LCModel RAW format, as specified in Chapter 5 of the User's Manual, can also be made using tools on the Internet or (for older data) using the recommended LCMgui GUI decribed below.
Only for brain: Basis sets of model metabolite spectra. (See Sections 9.2 and 9.3 of the manual for other organs.)

There is a Windows version, but without the GUI; you use Chapter 5 of the User's Manual

The source code 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 sample Makefile.

Please note:

Much of the rest of this website has not been updated since LCModel became free software.

Download, Install & Test:

You can freely download the complete LCMgui/LCModel package 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.

Past News:

LCModel Version 6.3.

Estimation of GABA with MEGA-PRESS.
Improved estimation of weaker metabolites, especially glutamine.
Improved analyses of muscle, lipid, breast and liver spectra.

LCModel Version 6.2. While the main application remains brain, options have been added for more primitive spectra:

Mainly water & lipids, as in fat and bone.
Water & lipids plus possibly choline, as in breast and liver.
LCModel Version 6.1 with new options, including analysis of muscle spectra, particularly for IMCL.
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.
Major new LCModel Version 6 with many new features, including:
Estimates of macromolecule and lipid contributions in normals and in pathologies (e.g., tumors) with strong lipid signals and without strong lipid signals.
Analyses of full 2D slices or rectangular 2D subsets of 2D or 3D MRSI data sets.

Features:

Fully automatic, non-interactive, operator-independent: time-domain data input, one-page summary output.
Fully developed, over 29 years, with spectra analyzed from a wide variety of scanners and field strengths at more than 1000 sites.

Methods are described in:

Stephen Provencher: Estimation of metabolite concentrations from localized in vivo proton NMR spectra. Magn Reson Med 30, 672 (1993).

User's Manual (you can always get the latest version here).

LCMgui Graphical User Interface

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:

Freely available for use with LCModel.
Simplified usage, often only with mouse clicks, in two steps:
1. Select the data with the File Selector;
2. Start LCModel (optionally checking and modifying any settings) in the Control Window.
Currently for the following (older) single-voxel data:
- Bruker fid files.
- GE 5.x Probe raw P-files and spectrum G-files.
- GE Probe raw P-files. Also for P-files with multi-channel (phased-array) data.
- Hitachi data: LCModel is part of the Hitachi software; no need to use LCMgui.
- Philips SDAT/SPAR pairs and enhanced DICOM files.
- Picker (later Marconi, now Philips) DUMP files.
- Siemens *rda files transferred from the syngo PC console and Siemens raw files from the (old) Numaris-3 Unix console.
- Toshiba rawData files and Version 7.xx (and later) DICOM files.
- Varian/Agilent fid files.
- Other data types using your own conversion script.
Currently for the following MRSI data:
- 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 LCModel Manual.)
  
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- Other data types using your own conversion script;
- For GE MRSI (and single-voxel) data, Mary McLean's SAGE/LCModel interface [MA McLean et al, Magn Reson Med 44, 401 (2000)] is integrated into GE's SAGE Research version (from SAGE Dev2002.1).

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