MRI template and connectivity matrix incompatible in dimensions?

For some reason I couldn't load it in Brainstorm while archived, but it worked after extracting the files.

It worked for me.
Either you already have a protocol with the exact same name in your database, or you do not have the write to create the folder Paper1_PN07_copy in the folder that is currently used as your "database folder".
(to see what this is, you can execute: bst_get('BrainstormDbDir'))

Please let me know if I can provide anything else, and thank you so much for all the help!

I found the bug... When creating the scouts from the AAL3 volume parcellation, it was trying to detect the lobe with a function working only for surface parcellations... You can see that in the scout tab, most scouts have their region that is incorrectly detected (the two letters at the left of the scout name).

I disabled this, and it seems to work already better. Now it should only show "L" or "R" in the Scout tab.
You need to create the atlases again and compute the source results again. Update Brainstorm to get the fix.

Thanks for finding and reporting this bug!