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app-maxwell-filter
- Aurore Bussalb (Unlicensed)
aPp under development PRIVATE APP ON BL
This App allows to apply Maxwell Filtering to MEG signals in order to reduce environmental noise. To do so, the MNE Python function mne.preprocessing.maxwell_filter is used.
Github repository:
https://github.com/AuroreBussalb/app-maxfilter
Brainlife datatype used:
For inputs: neuro/meg/fif and neuro/meg/fif-override
For outputs: neuro/meg/fif and report/html
Inputs of the App:
Files | Format | Datatype | Description | Optional |
|---|---|---|---|---|
MEG signals | .fif | meg/fif | Data to process | No |
Head position file | .pos | meg/fif-override or meg/fif | Compensates for head movements | Yes |
Fine calibration file | .dat | meg/fif | Encodes site-specific information about sensors orientation and calibration | Yes |
Cross talk compensation file | .fif | meg/fif | Reduces interference between Elekta’s co-located magnetometer and paired gradiometer sensor units | Yes |
Destination | .fif | meg/fif-override or meg/fif | Empty .fif file containing only the mean transformation matrix computed across all runs to realign all runs to the mean head position | Yes |
Channels | .tsv | meg/fif or meg/fif-override | BIDS compliant channels.tsv | Yes |
To obtain the reference run containing the mean transformation matrix computed across all runs, we can use the app-mean-transformation-matrix. It is also possible to obtain the head position file thanks to the app-head-pos and the channels.tsv with app-bad-channels
This headpos file can be obtained thanks to the app-head-pos (if so, the file will be linked to the meg/fif-override datatype) or can be directly available with the meg.fif in the meg/fif datatype. If there are two head.pos (one from meg/fif datatype and the other from meg/fif-override datatype, only the file from the meg/fif-override will be used (see How to use the meg/fif-override datatype).
This is the same issue with channels.tsv and destination.fif.
Outputs of the App:
Files | Format | Datatype | Description |
|---|---|---|---|
MEG signals | .fif | meg/fif | Data after Maxwell Filtering |
Report | .html | html |
|
Besides, in the output directory, there are the optional files that can be used in a next App (see How to run Apps one after another).
Parameters of the App
The parameters of the App correspond to the parameters passed to the Python functions used in the App. Their default values proposed in Brainlife or in config.json.example correspond to the default values of MNE Python 0.23.
Next improvements
Allow user to change the plot parameters for the plots in the HTML report?