Page Comparison

...

This issue, regarding bad channels, was also discussed here Où stocker l'information "bad channels", and it was decided that the App that detects bad channels will only returns a BIDS-compliant channels.tsv and this file will be used in other Apps to populate the raw.info['bads'].

Channels.tsv

Steps to create a BIDS compliant channels.tsv

...

The output datatype of the App that detects bad channels is meg/fif-override (see https://brainlife.io/datatype/608195ce89df435fd26893c1), but as pointed out here Où stocker l'information "bad channels", MNE Python functions used the info stored in raw.info['bads']. So, we need to update raw.info['bads']with the info of channels.tsv. If raw.info['bads'] is not compliant with the info of channels.tsv, a warning is displayed to the user to tell him that, by default, only bad channels from channels.tsv are considered as bad: the info of his MEG file will be updated with those channels. The comparison between channels.tsv and raw.info['bads'] is performed at the beginning of each App thanks to helper.py (see Create a helper.py file).

Events.tsv

The events info is stored in raw.info['events'], but this info shouldn’t be manually changed, it is changed by the MNE Python function:

...

1. Create a BIDS path using mne_bids

2. Get all the info needed to create the events file

3. if we create fixed length events: we need to extract the event id

if we extract existing events we use mne.read_events()

4. Convert the MEG file into a BIDS structure using mne_bids.write_raw_bids() and specify events_data and events_id

5. Extract the events.tsv from the BIDS path

6. Save it in the output directory

...

To create epochs we use the MNE function mne.Epochs() that takes as parameters the raw MEG file but also the matrix of events. So, we can’t give to this function the events.tsv directly, we need to extract the matrix of events from it.

...

Delete the BIDS folder created

To get BIDS compliant events.tsv and channels.tsv, we created a BIDS folder. When the Apps creating these files run on Brainlife, the BIDS folder, which is useless, is in the outputs files. Besides, its presence may be confusing for the App users:

...

So in main , we add the line:

rm -r bids

after running the app.