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Maxfilter

It is convenient to use a script to loop through your raw fif-files with MaxFilter. MaxFilter is installed on DANA.

Before measurement

  1. Copy the master /home/master/data_scripts/avg_headpos/maxfilter_avgHead.sh to your own directory.
  2. Change the settings in the headers to match your desired processing pipeline.
  3. Make executable

chmod u+x <your_file_name.sh>

! To check if the file is executable type ls -l <your_file_name.sh

During measurement

No action required

After measurement

  1. Run your personalized maxfilter script (cd into correct folder)

./<your_file_name.sh>

  1. When analysis is done, upload to server

Maxfilter names guide

  • sss: processed with Signal Space Separation.
  • tsss: processed with Temporal Signal Space Separation.
  • mc: applied movement correction.
  • ds: data is downsampled.
  • quat: quaternion; it has estimated the head movement but not done movement correction (this is represented in quaternion format).
  • avghead: TBA

Note

This pipeline is a wrapper for running Neuromag MaxFilter inside the NatMEG infrastructure at Karolinska Insitutet, Sweden (www.natmeg.se). Neuromag MaxFilter is a commercial software licenses by Electra Neuromag. The head position averagers are written in Python and use functions from MNE-Python (https://martinos.org/mne/stable/index.html). The pipeline has been tested to work on DANA, but no guarrantee is provided that it will work elsewhere!