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Though seemingly affected only by its immediate surrounding, the sphere of external influence extends to infinite distance. Nikola Tesla

Table of Contents

Prerequisite

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This tutorial teaches how to use the Maxfilter command line tool to remove artifacts on MEG signals coming from outside of the sphere of all MEG channels. This tool was build by Elekta, the vendor of our MEG.

It is also at this step that bad channels are marked and discarded (interpolated).

Step-by-step guide

  1. Choose a reference head position 
  2. Run Maxfilter on the raw data
  3. Check correction with Muse
  4. Iterate to fine tune correction parameters

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Code Block
maxfilter_cenir -f run01.fif -st 20000 -corr 0.98 -bad 0221 0332 -trans meanmeanhp.fif -o run01_tsss.fif

Brief description of the options (the user is referred to the pdf manual for more information):

  • -f: the input file
  • -o: the output file
  • -tsss: perform temporal source space separation (the standard at CENIR). The option is followed by a buffer length (in seconds), which should always be larger than your individual recordings.
  • -corr: amount of correlation between data and noise that should be rejected (see manual for more explanation). Lowering the value below the default 0.98 may sometimes help getting rid of artifacts but can also lead to removing interesting signal from the data. Careful inspection is recommended (see below).
  • -bad: which channels should be considered bad, i.e. removed prior to correction and later reinterpolated. The -autobad command is not recommended because it leaves no trace of which channels are considered bad. Rather use xscan (see below).
  • -trans: transforms the MEG data into the sensor array defined by the channel info in a specified file (here mean.fif).

 


Warning
titleuse maxfilter_cenir

Be sure to use the maxfilter_cenir command and NOT maxfilter. This will ensure that correct tuning parameters found in the sss_config directory next to your data are applied during the computation. The full script below spells out the full command for each file it runs on.


Info
titleIn case of large artifacts, be sure to check this

On rare occasions, we experienced some trouble with tsss processing: when large dc-offset is present in the signal at the beginning of the file a bug can occur, leaving the resulting file with strong artifacts at the beginning of the file and a lot of noise above 80Hz on a number of channels.

If you encounter this kind of behavior, the solution is simple, before running tsss you need to remove the large dc-offset with dataHandler:
dataHandler -rbr 1 1000 -new run02_dc_offset run02.fiff
and then your maxfilter command: (for instance)
maxfilter_cenir -gui -st 20000 -trans meanhp.fif -f run02_dc_offset.fif

This problem is quite rare. A possible cause is large low frequency artifacts happening during recording (for those working with patients having big metallic part, be careful!).

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After Maxfilter has finished, it is important to check signal quality visually. We use Muse to do this.

Code Block
muse run01_tsss.fif

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