Behavior and Neuroimaging Core User Manual
  • About
  • Infrastructure Overview
  • XNAT
    • Getting Started
    • Accessing XNAT
    • BIDS Ready Protocols
    • New XNAT projects
    • Uploading Data
    • Downloading Data
  • Demo Dataset
    • Introduction
    • How to access it
    • Protocol Information
    • Basic analysis example: checks task
  • XNAT to BIDS
    • Getting Started
    • XNAT2BIDS Software
    • Exporting to BIDS using Oscar
      • Oscar Utility Script
        • Running xnat2bids using default configuration
        • Running xnat2bids with a custom configuration
        • Syncing your XNAT project & Oscar data directory
        • Extra tools & features
      • Step-wise via Interact Session
    • BIDS Validation
      • Oscar
      • Docker
    • Converting non-MR data
      • Physiological data
      • EEG data
  • XNAT TO BIDS (Legacy)
    • Oscar SBATCH Scripts
  • BIDS and BIDS Containers
    • Introduction to BIDS
    • mriqc
    • fmriprep
    • BIDS to NIMH Data Archive (NDA)
  • Analysis Pipelines
    • Freesurfer
    • 🚧CONN Toolbox
    • FSL topup and eddy
    • Tractography: DSI Studio
    • Brown University MRS Data Collection and Preprocessing Protocol
    • LC Model
      • Installation
      • Example Run
      • Running LCModel on your own data
    • Quantitative Susceptibility Mapping (QSM)
  • Standalone Tools
    • Multi-session spectroscopy with voxalign
    • dicomsort: a tool to organize DICOM files
    • ironmap
    • convert enhanced multi-frame DICOMs to legacy single-frame
    • DICOM anonymization
  • MRF GUIDES
    • MRI simulator room
      • Motion Trainer: Balloon Task
      • Simulating scanner triggers
    • Stimulus display & response collection
    • Eyetracking at the scanner
    • Exporting data via scannershare
    • EEG in the scanner
    • Exporting spectroscopy RDA files
  • Community
    • MRF/BNC user community meetings
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  • Installing LCModel in Oscar
  • 0. Connecting to Oscar
  • 1. Download LCModel tar under your HOME
  • 2. Download LCModel binaries and uncompress file
  • 3. Run the installer script
  • 4. Install the License
  • 5. Copy the Basis Set

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  1. Analysis Pipelines
  2. LC Model

Installation

Installation of LCModel GUI

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Last updated 8 months ago

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Installing LCModel in Oscar

Installing LCModel in Oscar for personal use is a simple process. Because LCModel has a graphical interface, you will need to connect to Oscar using the Desktop Application via OpenOnDemand, this will make sure we are using a node that can find its $DISPLAY.

0. Connecting to Oscar

Connecting via Desktop App in Open on Demand

  • Visit

  • Click on the Desktop Icon and start a Desktop job. If you receive an error the error you are already running a Desktop session, you will need to click on "My interactive sessions" at the top panel on the page. You will see your existing session. Click Launch to start this session.

  • Launch a terminal inside the Desktop interface.

1. Download LCModel tar under your HOME

# change directory to your HOME 
cd ~

2. Download LCModel binaries and uncompress file

# download LCModel
wget http://s-provencher.com/pub/LCModel/programs/lcm-64.tar -O lcm-64.tar
# un-tar file
tar xf lcm-64.tar

3. Run the installer script

./install-lcmodel

At this point a GUI window will pop as follows:

Press Continue. A test report should show up as follows:

Close the result window. A new success window will follow

Finally, you can Exit LCMgui

You may see the following error message: Infiniband hardware address can be incorrect! Please read BUGS section in ifconfig(8). This should not have any effect. It is a known message in Oscar that will go away in a future update

4. Install the License

LCModel is now free. However, you'll need to create an empty license file. You can do so from the terminal as follows.

cd ~/.lcmodel
touch license

If you have used LCModel before and have an outdated license file, please remove it

5. Copy the Basis Set

cp -r /oscar/data/bnc/shared/lcmodel/basis-sets ~/.lcmodel/basis-sets

https://ood.ccv.brown.edu
LCModel Select PostScript Display or Print Command
LC Model Sample PostScript Result
Confirmation Screen for a Successful LCModel Test