Nirstorm problem

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1

Hello everyone,
As part of my thesis, I am conducting an fNIRS study and need to use NIRSTORM to process my data, but I am originally a neuropsychologist and have no experience in neuroimaging.

I am likely facing several issues:
-The compatibility of my .snirf files with NIRSTORM.
Here is the message I receive when I try to import my original files:

Mess_Error_Import_Brainstorm
Mess_Error_Import_Brainstorm1916×987 120 KB

I sent this same image to ChatGPT and here is its response: ChatGPT - Problème importation NIRS
So I transferred my data to MNE by re-saving it in .snirf format, and this is what I got (I save in pre-frontal format).

Visuel_NIRSTORM
Visuel_NIRSTORM405×587 31.8 KB

I don't know if the problem stems from the file conversion by MNE or if it's nothing and I just need to change a setting or something else.

I'm still trying to see how to perform the steps of my data quality check, but when I go to Plugins > NIRSTORM, I don't have a NIRSTORM toolbar, so there's no “Convert to ΔOD” icon. However, my NIRSTORM plugin seems to be installed. So I asked ChatGPT, and here's its response: ChatGPT - Problème barre d'outils NIRSTORM

But when I do:
plugin_nirstorm(‘Load’);
I get the following message: Unrecognized function or variable ‘plugin_nirstorm’.
I therefore think that NIRSTORM is probably not installed correctly, but the engineers in my lab are on vacation and I have no one to help me (I am leaving to process the data at the EPIC center in Montreal in September (I am in France) and I need to have completed the QC of the data before I leave).

This raises another problem: I have over 2,600 files, so I tried to write some code to identify files that might be problematic:

code_cq.m (2.1 KB)

Obviously, it doesn't work. My question is: does it not work because of my data OR because NIRSTORM is not installed correctly?

Thank you very much in advance for your help.

2

You may want to go into Plugins -> fNIRS and see if nirstorm is present. If it appears in your plugins it will have a grey circle next to it (not yet installed) or a red circle (unloaded).
If the circle is green then nirstorm is installed and the problem is something else.

I'm not sure ChatGPT is giving you good information on how to check this, I currently have Nirstorm installed and "plugin_nirstorm('Load');" is not a valid command.

3

Thank you for your feedback.
NIRSTORM is installed with a green circle.
Yes, I noticed, but I have never coded or used neuroimaging software, so I don't know which command is appropriate.
Has anyone ever created a code to identify data thas does not pass the quality check with NIRSTORM ?

4

It seems there is an issue on reading the channel information within this file.
Could you share a file that is giving you this error?

Be careful when using ChatGPT or other alike tools. While they are powerful AIs, they also tend to hallucinate code. That function does not exist, you can test to load NIRSTORM with:

>> bst_plugin('Load', 'nirstorm')

At first glance the shared code looks good. If it is not working, I'd suggest you the following:

  1. Sanity check: Try the same steps in the GUI with a couple of files.

  2. Debug your code, using the debugging tools in Matlab to see where and why it does not work:
    https://www.mathworks.com/help/matlab/matlab_prog/debugging-process-and-features.html
    https://www.youtube.com/watch?v=PdNY9n8lV1Y

  3. Before the first FOR loop in the code, you can add the following lines to Install/Load NIRSTORM and show the error message if any

    [isOk, errMsg, PlugDesc] = bst_plugin('Install', 'nirstorm');
if ~success
    error(errMsg)
end
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