LCModel¶
Description¶
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.
Environment Variables¶
- HPC_LCMODEL_DIR - installation directory
- HPC_LCMODEL_BIN - executable directory
Additional Usage Information¶
Note
Due to this application's design, HiperGator no longer supports module maintenance for LCModel. It's recommended that users install and run this software locally by following instructions posted on the LCModel Installation Page. 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.
Categories¶
biology, spectroscopy