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=Maxfilter= = Maxfilter =

Maxfilter

A common first step in analysing your data is to pre-processing them using the Maxfilter program. This Neuromag sofware implements "Signal-Space Separation" (SSS), which is a clever mathematical way to separate magnetic signals coming from within the brain (or more precisely, a sphere within the sensors) from those coming from outside the brain (or more precisely, from outside a sphere outside the sensors). Some PDFs that describe the SSS mathematics are here: attachment:Taulu_IEEE_05.pdf , attachment:Taulu_JAP_05.pdf , attachment:Taulu_PMB_06.pdf .

Maxfilter is essential if you have acquired your data using Maxshield (to remove the shielding effects). It is also helpful for 1) removing noise, particularly using its "temporal extension", 2) detecting bad channels, 3) realigning (interpolated) data after movement (provided you have used continuous HPI) and 4) moving the data to a standard space (e.g, across subjects).

Before you apply SSS, it is a very good idea to mark bad channels. These can be detected with the "autobad" feature of Maxfilter (though this does not work for timeperiods in which continuous HPI is active, which is why we often only start cHPI after about 20s, and see below for bugs associated with this option). We recommend to scan the channels by eye during acquisition, keep a list of bad channels, and mark them during acquisition. Afterwards, you can use an MEG analysis program to investigate you data. The best option available is mne_browse_raw which is a part of MNE suit available on the linux cluster. BESA can be used on windows, and EEGLab toolbox on matlab but you need to change the data format before reading it into these two. Once you know the bad channels, you can then tell this to maxfilter (-bad option, see below), or you can mark them in the actual FIFfile using a commandline utility mark_bad_fiff under /neuro/bin/util/. Eg:

/neuro/bin/util/mark_bad_fiff 632 741 2211 <filename.fif>

Maxfilter will identify the bad channels you marked in the fiff file, and will not use them in calculations. If you don't want a permanent mark in the files, then use -bad option in maxfilter itself.

CbuMeg: maxintro (last edited 2014-04-04 09:37:54 by RikHenson)