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That file desc-ICA_mixing_static.tsv is copied into the output directory without any name change or prefix addition and then the same content is also appropriately named in sub-01_desc_ICA_mixing.tsv
I don't see this as a major issue for this PR. The one problem I could see it happening is if someone is using another package to run ICA and sending those matricies to tedana. In that case, it would be their responsibility to appropriately name their mixing matrix files.
https://github.com/tsalo/tedana/blob/1b97294eaed4e7111aba6a807c4ece38472a7270/tedana/tests/test_integration.py#L304
That file
desc-ICA_mixing_static.tsv
is copied into the output directory without any name change or prefix addition and then the same content is also appropriately named insub-01_desc_ICA_mixing.tsv
I don't see this as a major issue for this PR. The one problem I could see it happening is if someone is using another package to run ICA and sending those matricies to tedana. In that case, it would be their responsibility to appropriately name their mixing matrix files.
That said, the supplied mixing matrix is copied without any checks on whether it's overwriting anything:
https://github.com/tsalo/tedana/blob/1b97294eaed4e7111aba6a807c4ece38472a7270/tedana/workflows/tedana.py#L519-L525
This should definitely include a check for
io_generator.overwrite
That could be added here or in a stand-alone PR.Originally posted by @handwerkerd in #963 (comment)
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