[export bids] Adds basic NIRS support #843
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Adds initial support for NIRS (Near-Infrared Spectroscopy) data processing within the BIDS export functionality. This includes: - Recognizing NIRS data based on channel types. - Extracting NIRS-specific metadata (optode counts). - Creating 'nirs' subfolder and using '_nirs' suffix. - Exporting data to the SNIRF format. - Generating an optodes coordinate file. - Creating an events TSV file.
Adds functionality to export Brainstorm channel files in the BIDS _channels.tsv format, specifically tailored for NIRS data. This enhancement supports the BIDS standard for NIRS data organization.
Adds coordinate system information in json format for NIRS data (ScanRAS exclusively). Improved export channel option using export_channel, replacing 'out_channel_bids'.
- Adds section of code to generate the .tsv file by calling out_nirs_channel - Fixes detector labels (previously labelled 'S' instead of 'D') - Changes channel type to NIRSCWAMPLITUDE, a valid BIDS raw data type. Potential improvement in future to add other valid data types.
- out_nirs_channel header explanation now uses the correct fields - process_export_bids CreateMegJson has been working, no need for this note.
- Checks datasettype is either 'raw' or 'derivative' - if not one of the two accepted values, defaults to 'raw' as per BIDS documentation and gives a warning.
- Adds 'FiducialsCoordinates' field with NAS, LPA, and RPA coordinates to coordsystem.json from ChannelMat.SCS - Sets other fiducials coordinate metadata fields in coordsystem.json
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ok. it's ready for review. There are still some issue with the coordinate system, but I will fix them in a following PR so we can address the coordinates for EEG/MEG and Nirs at the same time. I also want to move to matlab_bids to generate the file name and reoganize the process but in a other PR :) |
Edouard2laire
changed the title
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One thing i dont understand is why the fiducials are not preserved after export/import : 
Actually, our import for channel is kind of a mess and wrong for nirs. i am not sure how to fix it though.... I guess we need to have the script import the channel.tsv as it contains the info. but it also needs to read the json for the coordinate system. |
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ok. so exporting in CTF is somehow fixing the coordinates. |
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Note: I rebased the change from #812 to this branch so i can continue working on it while @JBusgang is busy with classes.