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ROIs in MNE are defined as "label" files. Freesurfer already creates a parcellation of the cortical surface in various regions of interest (see subdirectory "label" in your subjects' MRI directory). These can be converted to label files for MNE. You can then use mne_make_movie in order to extract amplitudes for these ROIs, e.g. for statistical analysis. You can also define your own ROIs. You can morph ROIs between different brains (e.g. from average brain to individual brains) using mne_morph_labels. The resulting amp-files can be processed in Matlab. The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the MNE manual, reading papers, and discussions with more experienced researchers.

If you've morphed all your individual STC-files to an average brain (called "average" in the example), you can create MNE-labels from these: This will result in files such as "fusiform-lh.label" in the MRI label subdirectory. These are text files that you can read into a text editor etc. Then you can extract ROI information using mne_make_movie. The following script does it for multiple subjects, conditions, labels and both hemispheres. The resulting *.amp-files are text files that you can read into Excel, Matlab etc.

If you create your own labels, the path name for the label files (--label) should be changed accordingly. 1) Display a cortical surface (and e.g. an STC file) in mne_analyze. 2) Define the borders of your ROI by defining points using your right mouse button. 3) Hold the "CTRL" key and click into the centre of your points with your right mouse button. 4) Save the label. 5) Use mne_make_movie to extract information for this label. Note that you can use mne_morph_labels to morph labels between subjects, for example to the average brain. This video shows how to load an existing STC file and use it to define your own ROI (you may have to download the movie and play it outside your browser).

The following Matlab script reads amp-files, and averages across vertices and within latency ranges. The output will be written to an Excel file or separate text files (note: Excel files can only be created under Windows, not Linux). As usual, there is not copyright but also no guarantee...