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 User 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.

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..

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 .

Mature software

This Section contains documentation for software components, which are still available in the MNE software but have been replaced by new programs.

mne_compute_mne

This chapter contains information about the options accepted by the program mne_compute_mne , which is gradually becoming obsolete. All of its functions will be eventually included to mne_make_movie , see Producing movies and snapshots. At this time, mne_compute_mne is still needed to produce time-collapsed w files unless you are willing to write a Matlab script of your own for this purpose.

mne_compute_mne accepts the following command-line options:

—version

Show the program version and compilation date.

—help

List the command-line options.

—inv <*name*>

Load the inverse operator decomposition from here.

—meas <*name*>

Load the MEG or EEG data from this file.

—set <*number*>

The data set (condition) number to load. The list of data sets can be seen, e.g., in mne_analyze , mne_browse_raw , and xplotter .

—bmin <*time/ms*>

Specifies the starting time of the baseline. In order to activate baseline correction, both --bmin and --bmax options must be present.

—bmax <*time/ms*>

Specifies the finishing time of the baseline.

—nave <*value*>

Specifies the number of averaged epochs in the input data. If the input data file is one produced by mne_process_raw or mne_browse_raw , the number of averages is correct in the file. However, if subtractions or some more complicated combinations of simple averages are produced, e.g., by using the xplotter software, the number of averages should be manually adjusted. This is accomplished either by employing this flag or by adjusting the number of averages in the data file with help of mne_change_nave .

—snr <*value*>

An estimate for the amplitude SNR. The regularization parameter will be set as . If the SNR option is absent, the regularization parameter will be estimated from the data. The regularization parameter will be then time dependent.

—snronly

Only estimate SNR and output the result into a file called SNR. Each line of the file contains three values: the time point in ms, the estimated SNR + 1, and the regularization parameter estimated from the data at this time point.

—abs

Calculate the absolute value of the current and the dSPM for fixed-orientation data.

—spm

Calculate the dSPM instead of the expected current value.

—chi2

Calculate an approximate statistic instead of the F statistic. This is simply accomplished by multiplying the F statistic by three.

—sqrtF

Take the square root of the or F statistic before outputting the stc file.

—collapse

Make all frames in the stc file (or the wfile) identical. The value at each source location is the maximum value of the output quantity at this location over the analysis period. This option is convenient for determining the correct thresholds for the rendering of the final brain-activity movies.

—collapse1

Make all frames in the stc file (or the wfile) indentical. The value at each source location is the norm of the output quantity at this location over the analysis period.

—collapse2

Make all frames in the stc file (or the wfile) identical. The value at each source location is the norm of the output quantity at this location over the analysis period.

—SIcurrents

Output true current values in SI units (Am). By default, the currents are scaled so that the maximum current value is set to 50 (Am).

—out <*name*>

Specifies the output file name. This is the ‘stem’ of the output file name. The actual name is derived by removing anything up to and including the last period from the end of <name> . According to the hemisphere, -lh or -rh is then appended. Finally, .stc or .w is added, depending on the output file type.

—wfiles

Use binary w-files in the output whenever possible. The noise-normalization factors can be always output in this format. The current estimates and dSPMs can be output as wfiles if one of the collapse options is selected.

—pred <*name*>

Save the predicted data into this file. This is a fif file containing the predicted data waveforms, see Predicted data.

—outputnorm <*name*>

Output noise-normalization factors to this file.

—invnorm

Output inverse noise-normalization factors to the file defined by the --outputnorm option.

—dip <*name*>

Specifies a dipole distribution snapshot file. This is a file containing the current distribution at a time specified with the --diptime option. The file format is the ASCII dip file format produced by the Neuromag source modelling software (xfit). Therefore, the file can be loaded to the Neuromag MRIlab MRI viewer to display the actual current distribution. This option is only effective if the --spm option is absent.

—diptime <*time/ms*>

Time for the dipole snapshot, see --dip option above.

—label <*name*>

Label to process. The label files are produced by tksurfer and specify regions of interests (ROIs). A label file name should end with -lh.label for left-hemisphere ROIs and with -rh.label for right-hemisphere ones. The corresponding output files are tagged with -lh- <data type .amp and -rh- <data type .amp , respectively. <data type> equals MNE for expected current data and spm for dSPM data. Each line of the output file contains the waveform of the output quantity at one of the source locations falling inside the ROI.

Note

The --tmin and --tmax options which existed in previous versions of mne_compute_mne have been removed. mne_compute_mne can now process only the entire averaged epoch.