Hi Charles,
You should not average MEG recordings at the sensor level as you do with EEG. The head is moving in a fixed array of sensors, therefore the same sensor is most likely not capturing the information from the same brain regions in two different runs. The proper way is to calculate your group averages at the source level. Select the same files in the Process1 tab, but select the “process sources” button on the left side of the panel.
This requires a first step of anatomy normalization (skip this if all your subjects are warped versions of the Colin27 brain): http://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects
Then, for your database organization, the default “inter-subject” node is very limited. It is used to store all the files generated by the Brainstorm processes from multiple subjects. But after calculating your averages, you can move them from (inter-subject) to somewhere else that makes more sense to you.
For instance: create two additional subjects for storing the averages of the subject groups, with your four conditions each.
To move the files: 1) CTRL+X/CTRL+V or 2) drag and drop or 3) right-click > File > Cut/Paste
When you calculate your averages at the source level, you don’t have the question of what is the “common” channel file / head model / source model.
Does it answer the question?
Francois