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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  • 0. Make sure you have installed LCModel
  • 1. Start a VNC session
  • 2. Launch Terminal
  • 3. Launch lcmgui
  • 4. Select sample Siemens data
  • 5. Select Basis
  • 6. Add License Key to Control Parameters
  • 7. Run LCModel

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  1. Analysis Pipelines
  2. LC Model

Example Run

An example of running LCModel on a test data set

PreviousInstallationNextRunning LCModel on your own data

Last updated 1 year ago

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0. Make sure you have installed LCModel

Every user must install LCModel for their own user. If you haven't, please refer to the

1. Start a VNC session

To run LCModel's GUI you will need to start . LCModel is not very resource intensive so you can request a basic session

2. Launch Terminal

  • Inside your VNC session, open a Terminal window.

  • Navigate to LCModel's hidden directory cd ~/.lcmodel

3. Launch lcmgui

  • To launch the lcmgui, simply type ./lcmgui from the current directory (~/.lcmodel)

  • Accept license agreement

4. Select sample Siemens data

  • Select Siemens at the data type prompt

  • Search for the share data: /oscar/data/bnc/shared/lcmodel/TestData.rda

5. Select Basis

During installation, the basis-set was installed under the LCModels' hidden directory in your home. i.e., $HOME/.lcmodel/basis-set which is equivalent to /oscar/home/$USER/.lcmodel/basis-set

  • Change the basis file to: $HOME/.lcmodel/basis-sets/press_te30_3t_gsh_v3.basis

6. Add License Key to Control Parameters

You will need to add a key to the Control Parameters. We do so as follows:

a. Open Advanced Setting Dialog

b. Select View/Edit Control Parameters.

A dialog will open

c. Add key to Control Parameters

Add key= 210387309 to the control parameters as shown in the figure below. Be careful to match spaces. When done, press OK

d. Save parameters file (optional)

LCModel will ask you if you want to save the new parameters to a new file. You can do so. If you do, the next time you can select the saved file from Advanced Settings -> Change Control-Defaults file

7. Run LCModel

After pressing Run LCModel, a two page PDF will appear, which looks as follows

Oscar's VNC Client
Installation Guide
Sample Terminal Window inside Oscar's VNC
Sample Data Type Window
Sample Data Browser Window
Sample Control Parameters Window
LCModel Result PDF - Page 1
LCModel Result PDF - Page 2