2nd level group analysis patients-controls

Hi,

I would need to define contrast and find statistical differences between two groups patients and controls during finger tapping task. Is there a tutorial to do this? I found how to analyze the differences between two conditions here

https://mne.tools/mne-nirs/auto_examples/general/plot_12_group_glm.html#sphx-glr-auto-examples-general-plot-12-group-glm-py

but I canâ€™t find group level analyses between two groups.

Could you help me?

Thank you,

• MNE version: latest
• operating system: e.g. macOS 11.6

@rob-luke, I have seen that you are the fNIRS expert. Do you have some suggestions?

Thank you

@mlrocca I think this is a pretty general statistics question, and not really specific to MNE-Python (or MNE-NIRS for that matter). What youâ€™re looking for is a two-sample test of some sort. Whether to do it with a scipy.stats.ttest_ind or something like a linear mixed-effects model is up to you, both are possible. Iâ€™d recommend looking into some statsmodels tutorials (esp. for mixed effects models) to see if people talk about use cases like yours

Hi @larsoner,

Actually, my question was not about the type of statistical test to choose but how to define a contrast between two groups for a certain condition in MNE. In other words how it is possible in MNE to define the design matrix and compute the GLM contrast for two groups.

Sorry if I was not very clear,

Could you help me out?

Thank you

In MNE you can pass any `stat_fun` and `threshold` that you want. So given that API, to me the two things you mention above are effectively the same thing â€“ you need to choose the statistical test to yield a test staistic (e.g., t or Z or F) value, and that alongside a reasonable threshold (or set of thresholds with TFCE) will allow you to do clustering.