Difference between revisions of "LCModel"

Latest revision as of 16:28, 15 December 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"):

Expand this section to view example file.

$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 36: / Line 36: @@
 <!--Run-->
 {{#if: {{#var: exe}}|==Additional Information==
 {{note|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"):===
+<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;">
+''Expand this section to view example file.''
+<div class="mw-collapsible-content" style="padding: 5px;">
   $LCMODL
   OWNER='Biomedizinische NMR Forschungs GmbH, Goettingen'
@@ Line 59: / Line 58: @@
   HZPPPM=84.47
   $END
+</div>
+</div>
 ===Tested using:===
   $ lcmodel < ./test.control
 |}}
 <!--Job Scripts-->
@@ Line 70: / Line 69: @@
 <!--Policy-->
 {{#if: {{#var: policy}}|==Usage Policy==
 WRITE USAGE POLICY HERE (Licensing, usage, access).
 |}}
 <!--Performance-->
 {{#if: {{#var: testing}}|==Performance==
 WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 |}}
 <!--Faq-->
@@ Line 86: / Line 81: @@
 {{#if: {{#var: citation}}|==Citation==
 If you publish research that uses {{#var:app}} you have to cite it as follows:
 WRITE_CITATION_HERE
 |}}
 <!--Installation-->