Difference between revisions of "LCModel"
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Johnbullard (talk | contribs) (Created page with "Category:Software Category:Neuroimaging {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|LCModel}} |{{#vardefine:url|http://s-provencher.com/lcmodel.shtml}} <!--CONF...") |
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[[Category:Software]] | [[Category:Software]] | ||
| − | [[Category: | + | [[Category:Biology]] |
| + | [[Category:spectroscopy]] | ||
| + | {|align=right | ||
| + | |__TOC__ | ||
| + | |} | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|LCModel}} | |{{#vardefine:app|LCModel}} | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#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:=== | ===Manual:=== | ||
http://s-provencher.com/pub/LCModel/manual/manual.pdf | http://s-provencher.com/pub/LCModel/manual/manual.pdf | ||
| − | |||
===Example control file ("test.control"):=== | ===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 | $LCMODL | ||
OWNER='Biomedizinische NMR Forschungs GmbH, Goettingen' | OWNER='Biomedizinische NMR Forschungs GmbH, Goettingen' | ||
| Line 52: | Line 58: | ||
HZPPPM=84.47 | HZPPPM=84.47 | ||
$END | $END | ||
| − | + | </div> | |
| + | </div> | ||
===Tested using:=== | ===Tested using:=== | ||
$ lcmodel < ./test.control | $ lcmodel < ./test.control | ||
| − | |||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
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<!--Policy--> | <!--Policy--> | ||
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
| − | |||
WRITE USAGE POLICY HERE (Licensing, usage, access). | WRITE USAGE POLICY HERE (Licensing, usage, access). | ||
| − | |||
|}} | |}} | ||
<!--Performance--> | <!--Performance--> | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | |||
WRITE_PERFORMANCE_TESTING_RESULTS_HERE | WRITE_PERFORMANCE_TESTING_RESULTS_HERE | ||
| − | |||
|}} | |}} | ||
<!--Faq--> | <!--Faq--> | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | |||
WRITE_CITATION_HERE | WRITE_CITATION_HERE | ||
| − | |||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
| − | {{#if: {{#var: installation}}|==Installation== | + | {{#if: {{#var: installation}}1|==Installation==}} |
| − | + | ||
<!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | <!--Turn the Table of Contents and Edit paragraph links ON/OFF--> | ||
| − | + | ||
| + | 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. | ||
Latest revision as of 16:28, 15 December 2022
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.
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.