Advice on Neuromag analysis
For some general information on Signal Space Projection (SSP), Signal Space Separation (SSS) and its temporal extension (tSSS), see here: http://www.megwiki.org/index.php?title=MEG_Analysis
Avoid split raw data files
If you recording takes more than 2GB, it will be automatically split into two (or more) files: filename.fif, filename-1.fif, etc. As consequence, you will (1) have to deal with very large files which take long time process, (2) your trial will be unevenely spread across two or more different files making it more cumbersome to average. To avoid this, make sure your blocks are within the 2GB limit. This is usually just above ~20 minutes with all 306 channels at the default 1kHz sampling rate, and under 12 min if you add 128 channels of EEG.
<Tip> Downsampling your data later by factors of 2-4 within Max Filter can save filespace and time (default sampling frequency is 1000Hz, but one is rarely interested in frequencies above 100Hz). One could of course change the default sampling frequency during acquisition, but be careful that some of the (continuous) Head Positioning Coils use frequencies of several hundred Hz.
The first step towards analysing your data is pre-processing it using Maxfilter utility. This is necessary regardless of the tools you are going to use for further analysis (ENM, SPM, Besa, etc.) More information about maxfiltering here.
More to follow here....