Example Run

An example of running LCModel on a test data set

0. Make sure you have installed LCModel

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

1. Start a VNC session

To run LCModel's gui you will nedd to start Oscar's VNC Client. 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
Sample Terminal Window inside Oscar's VNC

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
Sample Data Type Window
  • Search for the share data: /gpfs/data/bnc/shared/lcmodel/TestData.rda
Sample Data Browser Window

5. Select Basis

During installation, the basis-set was install under the LCModels' hidden directory in your home. i.e., $HOME/.lcmodel/basis-set which is equivalent to /gpfs/home/$USER/.lcmodel/basis-set
  • Change the basis file to: $HOME/.lcmodel/basis-sets/press_te30_3t_gsh_v3.basis
Sample Control Parameters Window

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. Becareful 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
LCModel Result PDF - Page 1
LCModel Result PDF - Page 2