fMRIPrep - normalisation using MNI152_T1_2mm_brain

1

Hi,

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!

2

Hi,

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!

Best,
Steven