how to read my own nirs file with MNE?

[shijian97]

I installed mne and mne-nirs, and I have some nirs file like "1.nirs"
I use raw_intensity = mne.io.read_raw_nirx('1.nirs', verbose=True), and there is OSError: Need a directory for fname but found a file at ".......\1.nirs".
Can you help me how to read my nirs file? and I want to use function mne.preprocessing.nirs.scalp_coupling_index with the raw data.

[drammock]

What device/software was used to record the data? Did you read through https://mne.tools/dev/auto_tutorials/io/30_reading_fnirs_data.html?

[sachinu25]

If your file is from another vendor (e.g., Hitachi, SNIRF, etc.), use the matching function:

SNIRF: mne.io.read_raw_snirf('file.snirf')

Hitachi: mne.io.read_raw_hitachi('file.csv')

[natinew77-creator]

Hi, I can help with this!

The OSError: Need a directory for fname but found a file... error is a very common issue when reading NIRx data.

The Problem:
The function mne.io.read_raw_nirx() is designed to read the parent directory that contains all the NIRx files (like .nirs, .hdr, etc.). It should not be given the path to a single file like 1.nirs.

The Fix:
Instead of passing the file path:

# This will cause an error
raw = mne.io.read_raw_nirx("/path/to/1.nirs")

Pass the folder path that contains the NIRx files:

# Correct usage
raw = mne.io.read_raw_nirx("/path/to/nirx_data_folder/")

Alternative:
If your data is in a different fNIRS format (like SNIRF), you may need to use a different reader function such as mne.io.read_raw_snirf().

Reference:
For more details, you can refer to the MNE-Python tutorial on Importing data from fNIRS devices.

I hope this helps!

[larsoner]

In principle we could try to be smart enough to use .parent in the case that .is_file() passes. But I think the error message we have is okay and this is more of a usage issue so I'll close. But if someone wants to improve the docs that's welcome!

[natinew77-creator]

Thanks for the feedback, @larsoner! I'd be happy to help improve the docs to make this clearer for users.

I could add a note to the read_raw_nirx docstring or the fNIRS tutorial clarifying that:

The function expects a directory path, not a file path
Common error messages and their solutions
Would a PR adding this clarification be welcome? I can work on it!