Using tutorial fNIRS scripts with NIRx fNIRS data

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  • MNE version: 1.0.dev0
  • operating system: macOS 11.4

I am trying to follow along the tutorial scripts provided for processing fNIRS data. However, my data output lacks some of the folders included in the sample data sets provided, for example, the ‘subjects’ folder. Additionally, my data is in the .nirs file format and I don’t know if that impacts how it gets processed.

Here is an example of the data I’m working with (whole-head recording with short channels and a movie watching paradigm): Dropbox - MovieDistSAMPLEDATA - Simplify your life

How would you advise that I could best modify the provided preprocessing scripts so that everything runs correctly?

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Hi @inichoso,

Thanks for trying MNE with your fNIRS data and sharing the test files, that makes it easier to see what you are working with.

First, some background details. Your data has been exported in the native nirx format and in the .nirs format. We will use the nirx format as it is better documented and works very well with MNE. The .nirs format is being phased out in favor of the better documented snirf format, but that is not something that will affect us here.

I was able to load your data by running the following commands…

import mne
raw = mne.io.read_raw_nirx("/path/MovieDistSAMPLEDATA/0F19372E_2021-12-09")
# Loading /Users/rluke/Downloads/MovieDistSAMPLEDATA/0F19372E_2021-12-09
# <ipython-input-2-b0c81c774a91>:1: RuntimeWarning: MNE has not been tested with Aurora version 2021.9.0-6-g14ef4a71

Then I was able to validate that the data looked sane by running

raw.plot()
raw.plot_sensors()

which resulted in

image
image1902×1020 377 KB

image
image625×703 46.4 KB

So it looks like you have a nice whole head coverage, I am very jealous.

I hope this helps, hopefully a simple modification to the tutorial to point to your data should be all that’s needed.

Please let us know if you get this working or not.

Regards,
Rob

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Hi Rob,

Thank you so much for your response. I implemented your suggestions and they worked perfectly.

Thanks again,
Isabel