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But, maybe the user will run the pipeline from the beginning and still provide the headshape.pos and channels.tsv in 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.
destination.fif is quite specific, we think that it will only be obtained with the app-mean-transformation-matrix, so we won’t have two versions of this file.
In the Python code, we first read the files from the meg/fif datatype:
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