Dear Edwardai,
> The thickness of MPRAGE is 1mm. Should I register them to MNI152_T1_2mm or MNI152_T1_1mm? Which is better?
the space you want to end up in depends on what you will ultimately use your data for. If the purpose is to register EPI data for group-level analysis then 2mm is enough. If you want to do detailed anatomical analysis you may want to go to 1mm.
>
> I know there is a configuration file of FNIRT(register to MNI152_T1_2mm) in FSL. Is there a configuration file about registeration to MNI152_T1_1mm?
I mostly recommend registering to the 2mm template (using the usual configuration file) and then resampling to the 1mm template with applywarp.
Good luck Jesper
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