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APP UNDER DEVELOPMENT PRIVATE APP ON BL

This app aims at computing the mean transformation matrix across all runs of a MEG session to correct the head position of all runs thanks to this matrix. This mean transformation matrix is stored in an empty .fif file, which then can be passed as a parameter in mne.preprocessing.maxwell_filter (destination parameter).

GitHub repository

https://github.com/AuroreBussalb/app-mean-transformation-matrix

Brainlife datatype used:

Inputs of the App:

Files

Format

Datatype

Description

Optional

MEG signal

.fif

meg/fif

first run

No

MEG signal

.fif

meg/fif

second run

No

…

…

…

…

Yes

MEG signal

.fif

meg/fif

nth run

Yes

At least two runs are required.

Output of the App:

Files

Format

Datatype

Description

Raw file

.fif

meg/fif-override

  • Info and fake data created

  • the mean transformation matrix is contained in raw.info["dev_head_t"]["trans"]

Besides, in the output directory, there are the optional files we will use in a next App. This is mandatory, because the App that will be run after app-mean-transformation-matrix will take as input all the files in app-mean-transformation-matrix’s output directory corresponding to the datatype of the input of the 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

  • Rename it into “app-compute-realigment-matrix”?

  • Allow the user to compute a destination.fif that is not the mean of all the runs but a specific run (this option is available is mne-bids-pipeline. To do so, it would be best not to save the entire .fif file (i.e. the MEG signals) but to extract the raw.info[“dev_head_t"]["trans"] from this run and put it in an empty fif file, like we do when we compute the mean of the runs (it would save space).

  • Make sure that it is okay to run this app after of before app-head-pos, the order must not matter.

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