Setup at the Martinos Center¶
Contents
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 Configuring MNE-C substituting /usr/pubsw/packages/mne/stable for <MNE> and /usr/pubsw/packages/matlab/current for <Matlab> . For most users, the default shell is tcsh.
Note
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..
Module |
Description |
---|---|
xfit |
Source modelling |
xplotter |
Data plotting |
graph |
General purpose data processor |
mrilab |
MEG-MRI integration |
seglab |
MRI segmentation |
cliplab |
Graphics clipboard |
Module |
|
---|---|
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
fromsubjects/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
orsample_audvis-ave.fif
(the on-line evoked-response average file) inMEG/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 .