How to do cluster-based permutation test of MEG data in group-level

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1
  • MNE version: 1.5.1
  • operating system: macOS Sonoma 14.3

Dear all,

I am now trying to do data analysis in Python-mne. But when I try to follow the turtorial “Spatiotemporal permutation F-test on full sensor data”, I faced an issue about group level analysis.

In my script, I save all my epochs’ data as list to achieve the group-level analysis. But when I try to concatenate the epochs with mne.concatenate_epochs function, the python report a bug as “ValueError: epochs[1].info[‘dev_head_t’] differs. The instances probably come from different runs, and are therefore associated with different head positions. Manually change info[‘dev_head_t’] to avoid this message but beware that this means the MEG sensors will not be properly spatially aligned. See mne.preprocessing.maxwell_filter to realign the runs to a common head position”.

Following the chatgpt suggestions, I set the dev_head_t to an identity matrix. But in the following analysis, I failed to get a signjficant result. Therefore, I am wondering whether my result is influenced by this setting because it seems that the position information is changed and is not accurate at all after doing this setting. But I don’t know how to analysis the group-level data without doing this. The tutorial only give the single data analysis, not in a group level.

Does anyone know is there any other template about group-level analysis? I am quite confused about this.

I will be really appreciated for your help.

Sincerely,

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Hi @Xindong,

Not an expert here, but as far as I know, setting the dev_head_t does not affect the analysis as long as you stay on sensor level. As soon as you move into the source space, it is not as easy anymore. (Maybe someone else can confirm this?)

Alternatively, which is also what I did when I encountered the same issue, you can try to extract the data from your epochs and continue your analysis with numpy arrays. Depending on what your goal is, you can actually get quite far withour relying on Epochs/Evokeds and alike.

Hope this helps,
Eduard