Difference between revisions of "LCModel"

Revision as of 22:15, 22 February 2022

Description

LCModel website

The LCModel package is for the automatic quantitation of in vivo proton MR spectra.

Environment Modules

Run module spider LCModel to find out what environment modules are available for this application.

System Variables

HPC_LCMODEL_DIR - installation directory

Additional Information

Due to this application's design, HiperGator does not longer support module maintenance for LCModel. It's recommended that users install and run this software locally by following instructions posted at http://s-provencher.com/lcm-test.shtml. For GUI use, follow instructions from an Open OnDemand terminal.

Manual:

http://s-provencher.com/pub/LCModel/manual/manual.pdf

Example control file ("test.control"):

$LCMODL
OWNER='Biomedizinische NMR Forschungs GmbH, Goettingen'
KEY(1)=0
TITLE='FIGURE 1:  Test Data (white matter, 2.0 T, STEAM, TE/TM=20/30 ms).'
ratipm = 2.0
ltable=7, filtab='/data/apps/tests/lcmodel/output/test.table'
lprint=6, filpri='/data/apps/tests/lcmodel/output/test.dump'
FILBAS='/data/apps/tests/lcmodel/output/test.basis'
FILRAW='/data/apps/tests/lcmodel/raw/test.RAW'
FILPS='/data/apps/tests/lcmodel/test.ps'
nameac(2)='NAAG'
neach=2  nameac(1)='NAA'
NUNFIL=2048, DELTAT=.0005
HZPPPM=84.47
$END

Tested using:

$ lcmodel < ./test.control

Installation

OOD desktop -> start a terminal

Get the lcm-64.tar file from http://s-provencher.com/pub/LCModel/programs/lcm-64.tar.

~$ wget http://s-provencher.com/pub/LCModel/programs/lcm-64.tar

Unpack lcm-64.tar

~$ tar xvf lcm-64.tar

Load evince pdf viewer

~$ ml ubuntu

Run the installer ~$ ./install-lcmodel

At this point you have ~/.lcmodel/bin/lcmodel and ~/.lcmodel/lcmgui.

Create symlinks to those executables in your ~/bin directory for convenience. Now, they are both in your $PATH and can be called on the command-line interactively or from job scripts.

@@ Line 87: / Line 87: @@
 |}}
 <!--Installation-->
-{{#if: {{#var: installation}}|==Installation==
+{{#if: {{#var: installation}}1|==Installation==}}
-See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 <!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
-__NOTOC____NOEDITSECTION__
+OOD desktop -> start a terminal
+Get the lcm-64.tar file from http://s-provencher.com/pub/LCModel/programs/lcm-64.tar.
+<code>~$ wget http://s-provencher.com/pub/LCModel/programs/lcm-64.tar</code>
+Unpack lcm-64.tar
+<code>~$ tar xvf lcm-64.tar</code>
+Load evince pdf viewer
+<code>~$ ml ubuntu</code>
+Run the installer
+<code>~$ ./install-lcmodel</code>
+At this point you have <code>~/.lcmodel/bin/lcmodel</code> and <code>~/.lcmodel/lcmgui</code>.
+Create symlinks to those executables in your <code>~/bin</code> directory for convenience. Now, they are both in your <code>$PATH</code> and can be called on the command-line interactively or from job scripts.