ENH: Agenda for fNIRS processing

The current status of NIRS support can be seen in this tutorial.

Here is a rough plan for the development of fNIRS processing in MNE.

Refactor existing code:

• Use write wavelengths to info['chs'][ii][loc][9] in addition to the channel name
• Use the info['chs'][ii][loc][9] value rather than channel names in preprocessing

Integrate fNIRS to existing MNE functions:

• Add support for hbo/hbr to plot_topomap
• Add support for hbo/hbr to plot_joint

Channel quality measures:

• Scalp coupling index. (#7215)

Add overlapping channel support to (these may already work with code changes I made, but don’t have tests if they aren’t ticked):

• topomap (#7414 )
• PSD topomap
• ICA topomap
• TFR topomap
• Projs topomap

Movement correction

• TDDR with MIT code to work from here (@larsoner and/or @rob-luke)

Interpolation of bad channels:

• Replace with nearest
• More intelligent interpolation

File support:

• Add SNIRF reader #7972
• Add SNIRF writer
• Add BIDS support
• Add NIRSport1 file reader
• Add NIRSport2 file reader (low priority as device will soon export in SNIRF format)
• Add Artinis file reader

Implement HRF GLM style analysis Moved to MNE-NIRS till mature enough to merge in Source Analysis Moved to MNE-NIRS till mature enough to merge in

[larsoner]

Why does NIRx.py apply the transform ahead of time? Instead of leaving it up to the user?

Channel locations in MNE-Python are supposed to be stored in Neuromag head coordinates, see:

https://mne.tools/dev/auto_tutorials/source-modeling/plot_source_alignment.html https://mne.tools/dev/overview/implementation.html#the-forward-solution

So the read_raw_nirx transforms them to the head coordinate frame. Since the NIRx are in MNI (apparently?) and fsaverage is in MNI, you can just use fsaverage’s standard transformation to get them to (fsaverage) head coordinates.

[agramfort]

give me admin access to your repo and I’ll do the transfer