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Maxfilter script for NatMEG

This is the process describing how to use the maxfilter script for NatMEG. The script is designed to run on a computer with a MaxFilter™ installation. The head position averagers are written in Python and use functions from MNE-Python. The pipeline has been tested to work on Cerberos at NatMEG, but no guarrantee is provided that it will work elsewhere!

You can find the necessary python scripts here

Prerequisits

Ensure you have the following non-default libraries installed in your Python environment: mne, matplotlib

Process

Install requirements

  1. Make sure python modules are installed in the environment. If not, install them using the following commands:
conda install mne matplotlib

Run script

Option 1. Run the script by executing the following command:

python maxfilter.py --config=path/to/maxfilter_settings.json
This will run the script with the config file wihout further questions.

Option 2. Edit config file before running the script:

python maxfilter.py --config=path/to/maxfilter_settings.json --edit
This will open a dialog for you to edit the config file before running the script.

Option 3. Run the script without a config flag 

python maxfilter.py # (add --edit to also edit an existing file)
You will get three options in the terminal - open: Open an existing config file (default) - new: Create a new config file from a default template using the dialog - cancel: Cancel the operation

Config file

{
"standard_settings": {
    "project_name": "",
    "trans_conditions": ["task1", "task2"],
    "trans_option": "mne_continous",
    "merge_runs": "on",
    "empty_room_files": ["empty_room_before.fif", "empty_room_after.fif"],
    "sss_files": ["empty_room_before.fif", "empty_room_after.fif"],
    "autobad": "on",
    "badlimit": 7,
    "bad_channels":[""],
    "tsss_default": "on",
    "correlation": 0.98,
    "movecomp_default": "on",
    "data_path": "."
    },

"advanced_settings": {
    "force": "off",
    "downsample": "off",
    "downsample_factor": 4,
    "apply_linefreq": "off",
    "linefreq_Hz": 50,
    "scripts_path": "/home/natmeg/Scripts",
    "cal": "/neuro/databases/sss/sss_cal.dat",
    "ctc": "/neuro/databases/ctc/ct_sparse.fif",
    "dst_path": "neuro/data/local",
    "trans_folder": "headtrans",
    "log_folder": "log",
    "maxfilter_version": "/neuro/bin/util/mfilter",
    "MaxFilter_commands": "",
    }
}

Standard_settings:

  • project_name: Name of the project
  • trans_conditions: List of conditions to be transformed
  • trans_option: Type of transformation (continous or initial)
  • merge_runs: Estimate head position average over all runs if multiple
  • empty_room_files: List of empty room files
  • sss_files: List of SSS files
  • autobad: Turn on or off autobad
  • badlimit: Bad limit
  • bad_channels: List of bad channels
  • tsss_default: Turn on or off tSSS
  • correlation: Correlation limit
  • movecomp_default: Turn on or off movecomp
  • data_path: Path to the data

Advanced_settings:

  • force: Force maxfilter to run
  • downsample: Downsample data
  • downsample_factor: Downsample factor
  • apply_linefreq: Apply line frequency filter
  • linefreq_Hz: Line frequency in Hz
  • scripts_path: Path to the script
  • cal: Path to the calibration file
  • ctc: Path to the crosstalk file
  • dst_path: Path to the destination folder (not active yet)
  • trans_folder: Name of the transformation folder
  • log_folder: Name of the log folder
  • maxfilter_version: Path to the maxfilter version
  • MaxFilter_commands: Additional commands for maxfilter (see MaxFilter manual)