Thanks Francois for those links. I was able to go through them and apply what I learned to the tmegpreproc files. I compared the output from the raw pipeline to the output of applying the source estimation step and on in that HCP-MEG tutorial to the tmegpreproc data and can confirm the brain maps match up as expected. Additionally, I can see how the fiducials, head model, and helmet are properly aligned in for the tmegpreproc data so long as you start from the source estimation step. Thanks for the help on that.
Now I need to export the source localized data but am having two problems. 1) I imported the data as a fif file since I had previously further cleaned the data in MNE-python. This seems to have caused me to lose the markers that differentiate a 0-back epoch from a 2-back epoch in the working memory dataset. Is this info recoverable, or is there a different way I need to import the data from the start?
2) exporting epochs seems to give me two options, either each epoch is saves as its own edf file (or other file type of my choosing), or the hole structures is saves as a zip file in a way that is only readable by brainstorm. Is there a different way to export the data that would have all the epochs in a single file that is readable by MNE or eeglab?
Thanks again for your help,
Matt