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sccn / xdf

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What needs to be done to make xdf an official format for BIDS? #24

Open cboulay opened 6 years ago

cboulay commented 6 years ago

Here is the relevant text from the BIDS BEP006: BIDS-EEG extension proposal.

While there are many file formats to store EEG data, there are 2 prefered formats in BIDS EEG: European data format (.edf) and BrainVision (.vhdr, .vmrk, .eeg) by Brain Products. There are also 3 additional ‘supported’ formats: EEGLAB set files (.set, .fdt), Neuroscan CNT (.cnt) and Biosemi (.bdf). The current selection is based on interoperability (one of the FAIR principles) between the main open source MEEG software, i.e. EEGLAB, FieldTrip (which supports SPM), Brainstorm and MNE Python. Note that most manufacturers’ software offers options to convert to .edf and original data format can be stored in the /sourcedata folder (see below).

Future versions of BIDS may extend this list of supported file formats (in particular for /derivatives). File formats for consideration MUST have open access documentation, MUST have open source implementation for both reading and writing in at least two programming languages and SHOULD be widely supported in multiple software packages. Other formats that may be considered in the future should have a clear added advantage over the existing formats and should have wide adoption in the BIDS-EEG community.

Please volunteer to take on any of these items.

sappelhoff commented 6 years ago

+1!

regarding point 1, I think that a pure python implementation is preferable, because it is easier to understand for a larger audience (there are fewer people who can read and understand C / C++ code)

regarding point 2, please see: https://github.com/mne-tools/mne-python/issues/5180

dmedine commented 6 years ago

I said a long time ago that I would shove xdf into MNE. The issue there (if I understand correctly) is that if there are multiple streams, they all have to have the same sampling rate, first time-stamp, etc. This makes it labor intensive enough for me to avoid doing it.

However, if MNE is like EEGLab and it is content to grab only EEG and marker streams, then this might not be such a chore after all.

The BIDS people are coming to Brain Products in December. Hopefully I will also be there at that time and can discuss this with them personally.

tstenner commented 5 years ago

With #19 the plain python reader's speed is within an order of magnitude compared to a pure C++ implementation so there's no binary extension / Cython magic needed (same for Matlab).

arnodelorme commented 5 years ago

I think this is the route:

DominiqueMakowski commented 1 year ago

Sorry to revive this thread, but I am currently trying to upload data acquired with LSL / LabRecorder to OpenNeuro but it doesn't seem to like .xdf files... Was there by any chance any progress on this front?

cboulay commented 1 year ago

@DominiqueMakowski , not as far as I know. I think your best bet is to convert the XDF files to a BIDS format.

DominiqueMakowski commented 1 year ago

Assuming my xdfs contains bodily signals (ECG, RSP) and EEG (from muse), any wild guess about what would the best way to do that?

I am thinking to open the xdf files, separate the eeg from the physio, save the former as .edf and the later as .tsv.gz, but maybe there's something more straightforward

cboulay commented 1 year ago

Just replying to let you know that I'm not a BIDS expert and I think you'll get a better answer in a BIDS forum. Do you use EEG-BIDS with sidecar files? Do you use two parallel BIDS folders? I don't know.

DominiqueMakowski commented 1 year ago

Fair enough, I'm still new to this so I don't have a good grasp of the ecosystem yet Thanks for your help, though, looking forward to seeing how xdf evolves :)