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  1. events.tsv and channels.tsv are BIDS compliant, see How to create a BIDS compliant channels.tsv and events.tsv files.

  2. An updated events.tsv is also returned by app-resampling when this app is applied to continuous data, and when an events.tsv is given in input. But the output of this app has not the meg/fif-override datatype because it returns also a meg.fif.

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For instance, the app-maxwell-filter takes as inputs the meg/fif datatype (for the meg.fif) and also optionaly optionnaly the meg/fif-override datatype. The inputs from the meg/fif-override datatype are optional because we don’t know if an App user will run the whole pipeline on Brainlife (i.e. compute the destination.fif, then the headshape.pos, detect bad channels, and eventually run Maxwell filter), maybe he will want to run only the app-maxwell-filter and he will provide the headshape.pos and channels.tsv without computing them with the BL Apps, and these files will be directly into the data staged under the meg/fif datatype.

But, maybe the user will run the pipeline from the beginning and still provide the headshape.pos and channels.tsv in when the data is staged underr the meg/fif datatype. So, for app-maxwell-filter we will have two versions of each file. So, in this case, only the files computed by the BL Apps will be taken into account.

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We decided not to inform the App user that the optional file previously computed by an App (so a file from the meg/fif-override datatype) will overwrite the optional file linked to the meg/fif datatype because we supposed that, if the User computed computes a new file he doesn’t want to use the file he gave at first when the data was staged.

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Info

The config.json keys for the meg/fif-override datatype don’t correspond to the name of the files they point to: it’s not an issue henceforth the file is saved with the good name when the App is run (shutil.copy2(destination_override, os.path.join(out_dir_name, 'destination.fif')), see How to run Apps one after another)

In the config.json created by BL we will have the keys linked to the meg/fif-override datatype, but these keys won’t be present if the App is run locally because the datatype issue is specific to BL (that’s why we check if the key is present at the beginning.

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