Setup at the Martinos Center

This Appendix contains information specific to the Martinos Center setup.

User environment

In the Martinos Center computer network, the 2.7 version of MNE is located at /usr/pubsw/packages/mne/stable. To use this version, follow Setting up MNE-C environment substituting /usr/pubsw/packages/mne/stable for <MNE> and /usr/pubsw/packages/matlab/current for <Matlab> . For most users, the default shell is tcsh.


A new version of MNE is build every night from the latest sources. This version is located at /usr/pubsw/packages/mne/nightly.

Using Neuromag software

Software overview

The complete set of Neuromag software is available on the LINUX workstations. The programs can be accessed from the command line, see Principal Neuromag software modules.. The corresponding manuals, located at $NEUROMAG_ROOT/manuals are listed in List of Neuromag software manuals..

Principal Neuromag software modules.
Module Description
xfit Source modelling
xplotter Data plotting
graph General purpose data processor
mrilab MEG-MRI integration
seglab MRI segmentation
cliplab Graphics clipboard
List of Neuromag software manuals.
Module pdf
xfit XFit.pdf
xplotter Xplotter.pdf
graph GraphUsersGuide.pdf GraphReference.pdf
mrilab Mrilab.pdf
seglab Seglab.pdf
cliplab Cliplab.pdf

To access the Neuromag software on the LINUX workstations in the Martinos Center, say (in tcsh or csh)

source /space/orsay/8/megdev/Neuromag-LINUX/neuromag_setup_csh

or in POSIX shell

. /space/orsay/8/megdev/Neuromag-LINUX/neuromag_setup_sh

Using MRIlab for coordinate system alignment

The MEG-MRI coordinate system alignment can be also accomplished with the Neuromag tool MRIlab, part of the standard software on Neuromag MEG systems.

In MRIlab, the following steps are necessary for the coordinate system alignment:

  • Load the MRI description file COR.fif from subjects/sample/mri/T1-neuromag/sets through File/Open .
  • Open the landmark setting dialog from Windows/Landmarks .
  • Click on one of the coordinate setting fields on the Nasion line. Click Goto . Select the crosshair tool and move the crosshair to the nasion. Click Get .
  • Proceed similarly for the left and right auricular points. Your instructor will help you with the selection of the correct points.
  • Click OK to set the alignment
  • Load the digitization data from the file sample_audvis_raw.fif or sample_audvis-ave.fif (the on-line evoked-response average file) in MEG/sample through File/Import/Isotrak data . Click Make points to show all the digitization data on the MRI slices.
  • Check that the alignment is correct by looking at the locations of the digitized points are reasonable. Adjust the landmark locations using the Landmarks dialog, if necessary.
  • Save the aligned file to the file suggested in the dialog coming up from File/Save .