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yjmantilla / sovabids

A python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata.
https://sovabids.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
9 stars 3 forks source link

Have an option to use symbolic links for raw data files #32

Open civier opened 3 years ago

civier commented 3 years ago

A suggestion by Brad Moffat (one of the NIF fellows): Provide an option to build the BIDS output with symbolic links to the original raw files (rather than copy them to the BIDS directory tree). This would allow to save on storage. It is also much more relevant to EEG than MRI, because in MRI you usually combine the DICOMS into NIFTI. In EEG, we will often leave them as-is (given that BIDS EEG supports 3 different raw data formats). I don't think there is anything equivalent in Windows (unless MNE-python or any of the other tools supports Windows's akward links), but should be easy to implement on Linux and Mac.

civier commented 2 years ago

Hello @bradmoffat, I'm tagging you on this thread

Thanks for completing the survey, and you're welcome to also open an issue with your suggestion regarding "a way for radiographers / researchers to use the comments dicom tag to add further info about BIDs formatting." Although you refer to MRI data, the same can be done with comment fields in EEG data. Best if you can give example of what you mean exactly.

yjmantilla commented 2 years ago

Provide an option to build the BIDS output with symbolic links to the original raw files (rather than copy them to the BIDS directory tree). This would allow to save on storage.

For me it seems a really particular feature which may not be easy to implement, mostly because the one doing the conversion (actual file copying and so on) is mne-bids . We would need to either pull the feature there or work-around the copies mne-bids did. Moreover, this would only be possible if there was only copying of files involved ( ie no conversion to another format).