fMRIPrep - normalisation using MNI152_T1_2mm_brain


Apologies for the simple question, I’m finding it difficult to get my head around the usage documentation!

I know the default brain atlas for spatial normalisation is the MNI152NLin6Asym, however is there a flag I could use to change this to the MNI152_T1_2mm_brain (or any other template that is compatible with FSL).

Thank you in advance!


Can you explain what you mean by “compatible with FSL”? FSL does use MNI 152 NLIN 6th Generation, Asymmetric, which is what is specified in fMRIPrep. If you are doing a group analysis in FSL, everything should be fine as long as your normalization is consistent across subjects. If you want to specify 2mm isotropic spacing you can add --output-spaces MNI152NLin6Asym:res-2 to your command. If you have another template in mind you can look at the templateflow repository. Hope this helps!