The sample data set¶

Structural MRIs¶

To set up the structural MRIs for processing with the Neuromag MRI viewer, MRIlab, say

mne_setup_mri

This command sets up the directories subjects/sample/mri/T1-neuromag and subjects/sample/mri/brain-neuromag . For more information, see Setting up anatomical MR images for MRIlab.

Source space¶

The source space with a 5-mm grid spacing is set up by saying:

mne_setup_source_space --ico -6

This command sets up the source-space related files in directory subjects/sample/bem as described in Setting up the source space.

Boundary-element models¶

The geometry calculations for the single-layer boundary-element model are accomplished with the command:

mne_setup_forward_model --homog --surf --ico 4

This command sets up the homogeneous BEM-model related files in directory subjects/sample/bem as described in Setting up the boundary-element model. In addition to the homogeneous BEM, you also need the three-layer BEM model, which can be used for both EEG and MEG:

mne_setup_forward_model --surf --ico 4

The above commands employ the inner_skull.surf , outer_skull.surf , and outer_skin.surf triangulation files located in subjects/sample/bem . The option --ico 4 will create a model with 5120 triangles on each surface. Depending on the speed of your computer, the three-layer model may take quite a while to set up.

Using the averaging script interactively¶

You can invoke an averaging script in mne_browse_raw from Process/Average… . Select the audvis.ave script from the file selection box that appears. Once averaging is complete, you can inspect the details of the averaged responses in the Averages window, which appears automatically. You can redisplay it from Windows/Show averages… . The window, which appears when you select Adjust/Manage averages… allows you to:

• Select which conditions (categories) are displayed.
• Change the trace colors.
• Inspect the averaging log.
• Save the averaged data.
• Delete this set of averages.

Using the averaging script in batch mode¶

The batch-mode version of mne_browse_raw , mne_process_raw can be used for averaging as well. Batch mode averaging can be done with the command:

mne_process_raw --raw sample_audvis_raw.fif `` ``--lowpass 40 --projoff `` ``--saveavetag -ave --ave audvis.ave

See mne_process_raw for command-line options.

As a result of running the averaging script a file called sample_audvis-ave.fif is created. It contains averages to the left and right ear auditory as well as to the left and right visual field stimuli.

Loading the averages¶

mne_browse_raw loads all the available data from an average file at once:

• Select Open evoked… from the File menu.
• Select the average file sample_audvis-ave.fif file from the list and click OK .
• A topographical display of the waveforms with gradiometer channels included appears.

Inspecting the auditory data¶

Select the left and right ear auditory stimulus responses for display:

• Select Manage averages… from the Adjust menu.
• Click off all other conditions except the auditory ones.

Set the time scale and baseline:

• Select Scales… from the Adjust menu.
• Switch off Autoscale time range and set the Average time range from -200 to 500 ms.
• Switch on Use average display baseline and set Average display baseline from -200 to 0 ms.
• Click OK .

You can display a subset of responses from the topographical display by holding the shift key down and dragging with the mouse, left button down. When you drag on the response with just the left button down, the signal timing, and channel name are displayed at the bottom. If the left mouse button is down and you press shift down the time is give both in absolute units and relative to the point where shift was pressed down.

Observe the following:

• The main deflection occurs around 100 ms over the left and right temporal areas.
• The left-ear response (shown in yellow) is stronger on the right than on the left. The opposite is true for the right-ear response, shown in red.

Inspecting the visual data¶

Go back to the Manage averages… dialog and switch all other conditions except the visual ones.

Observe the following:

• The left and right visual field responses are quite different in spatial distribution in the occipital area.
• There is a later response in the right parietal area, almost identical to both visual stimuli.

Initial alignment¶

Follow these steps to make an initial approximation for the coordinate alignment.

• Go to directory MEG/sample .
• Launch mne_analyze
• Select File/Load digitizer data… and load the digitizer data from sample_audvis_raw.fif .
• Load an inflated surface for subject sample from File/Load surface…
• Bring up the viewer window from View/Show viewer…
• Click Options… in the viewer window. Make the following selections:
  • Switch left and right cortical surface display off.
  • Make the scalp transparent.
  • Switch Digitizer data on.
• After a while, the digitizer points will be shown. The color of the circles indicates whether the point is inside (blue) or outside (red) of the scalp. The HPI coils are shown in green and the landmark locations in light blue or light red color. The initial alignment is way off!
• Switch the Digitizer data off to get the big circles out of the way.
• Bring up the coordinate alignment window from Adjust/Coordinate alignment…
• Click on the RAP (Right Auricular Point) button. It turns red, indicating that you should select the point from the viewer window. Click at the approximate location of this point in the viewer. The button jumps up, turns to normal color, and the MRI coordinates of the point appear in the text fields next to the button.
• Proceed similarly for the other two landmark points: Nasion and LAP (Left Auricular Point).
• Press Align using fiducials . Notice that the coordinate transformation changes from a unit transformation (no rotation, no origin translation) to a one determined by the identified landmark locations. The rotation matrix (upper left 3 x 3 part of the transformation) should have positive values close to one on the diagonal. Three is a significant rotation around the x axis as indicated by elements (3,2) and (2,3) of the rotation matrix. The x and y values of the translation should be small and the z value should be negative, around -50 mm. An example of an initial coordinate transformation is shown in Example of an initial coordinate alignment..
• Make the Digitizer data again visible from the options of the viewer window. Note that the points are now much closer to the scalp surface.

Example of an initial coordinate alignment.

Refining the coordinate transformation¶

Before proceeding to the refinement procedure, it is useful to remove outlier digitizer points. When you rotate the image in the viewer window, you will notice that there is at least one such point over the right cheek. To discard this point:

• Click on Discard in the Adjust coordinate alignment window.
• Enter 10 for the distance of the points to be discarded.
• Click done. The outlier point disappears.

The coordinate transformation can be adjusted manually with the arrow buttons in the middle part of the Adjust coordinate alignment dialog. These buttons move the digitizer points in the directions indicated by the amount listed next to each of the buttons.

An automatic iterative procedure, Iterative Closest Point (ICP) matching is also provided. At each iteration step

• For each digitizer point, transformed from MEG to the MRI coordinate frame, the closest point on the triangulated surface is determined.
• The best coordinate transformation aligning the digitizer points with the closest points on the head surface is computed.

In step 2 of the iteration, the nasion is assigned five times the weight of the other points since it can be assumed that the nasion is the easiest point to identify reliably from the surface image.

The ICP alignment can be invoked by entering the desired number of iterations next to the ICP align button followed by return or simply pressing the ICP align button. The iteration will converge in 10 to 20 steps.

Saving the transformation¶

To create a MRI fif description file which incorporates the coordinate transformation click Save MRI set in the Adjust coordinate alignment dialog. This will create the MRI set file in the $SUBJECTS_DIR/sample/mri/T1-neuromag/sets directory, which was created by mne_setup_mri_data , see Structural MRIs. The file will be called

COR- <username>- <date>- <time> .fif

where <username> is your login name.

You can also save transformation to a fif file through the Save… button. If the file does not exist, it will only contain the coordinate transformation. If the file exists it will be inserted to the appropriate context. An existing transformation will not be replaced unless Overwrite existing transform is checked in the save dialog.

Once you have saved the coordinate transformation, press Done and quit mne_analyze (File/Quit ).

Getting started¶

Launch mne_analyze . Select Help/On GLX… , which brings up a window containing Open GL rendering context information. If first line in the information dialog that pops up says Nondirect rendering context instead of Direct rendering context you will experience slow graphics performance. To fix this, your system software, graphics adapter or both need to be updated. Consult a computer support person for further information.

Load surfaces¶

It is reasonable to start the analysis by loading the display surfaces: choose the inflated surface for subject sample from the dialog that appears when you select File/Load surface… .

Load the data¶

Select File/Open… . Select sample_audvis-ave.fif as your data file and select the Left auditory data set. Select the inverse operator sample_audvis-ave-oct-6-meg-eeg-inv.fif and press OK . After a while the signals appear in the sample waveform and topographical displays. Click on the N100m peak in the auditory response. A dSPM map appears in the main surface display.

Show field and potential maps¶

Select Windows/Show viewer… . After a while the viewer window appears. Click on the N100m peak again. Once the field map preparation computations are complete, the magnetic field and potential maps appear. Investigate the viewer window options with help of The viewer.

Show current estimates¶

The options affecting the current estimates are accessible from Adjust/Estimate parameters… . With help of Working with current estimates, investigate the effects of the parameter settings.

Labels and timecourses¶

While in directory MEG/sample , create a directory called label :

mkdir label

Using the information in Creating new label files, create two labels A-lh.label and A-rh.label in the approximate location of the left and right auditory cortices. Save these labels in the newly created label directory.

Load all labels from the label directory and investigate the timecourses in these two labels as well as at individual vertices. Information on label processing can be found from Inquiring timecourses.

Morphing¶

Goto to $SUBJECTS_DIR and create the directory morph-maps . Load the inflated surface for subject morph as the morphing surfaces. Try switching between the original and morphing surfaces. More information about morphing is available in Morphing and in Morphing and averaging.

There is also a left-hemisphere occipital patch file available for subject morph . Load a righ-hemifield visual response instead of the auditory one and investigate mapping of the current estimates on the patch.