GLM analysis for grey matter only


Can I please get an expert opinion or any input on the analysis I’m implementing?
I want to run the GLM analysis for the grey matter only to reduce the number of voxelwise comparisons.
My data are preprocessed with fmriprep, so the volumes are in the MNI space.
For the first level analysis (FirstLevelModel in nilearn) I provide a MNI grey matter mask (loaded with fetch_icbm152_brain_gm_mask()).
Does it look plausible overall? Is it ok to use a standard MNI grey mask for all subjects or is it better to use the segmentation for each subject from fmriprep called space-MNI152NLin2009cAsym_label-GM_probseg (it’s in the anatomy folder)?
Is it better to run the first level on the entire brain and use a mask at the second level?

Thanks in advance :slight_smile:


In my view, it is perfectly reasonable to run the glm analysis on the MNI grey matter mask (and indeed, it makes sense to impose the same mask for all subjects).
The only motivation not to do that would be to check for possible distortions/artefacts, that are better seen if you don’t mask the data a priori.

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