fMRIPrep T1 and functional masks are not the same!

Hi everyone,

I had a fMRIPrep process. Do you know why T1 mask is not the same as functional mask? Does something wrong happen?
Please see attached photo:
blue: standardized T1 mask
red: standardized functional mask
violet: coverage of them


Hi @majidsaberi ,

It is completely normal, those two masks come from two different calculations based on two different images:

  • the anatomical mask is calculated from the T1w image through FreeSurfer.
  • the functional mask is is calculated from FSL bet and AFNI 3dAutomask on the functional image.

Due to the very different properties of the 2 images (high signal from CSF and dropout on the functional image notably), it is not surprising to understand that the masks end to to be quite different.

These two masks have different purposes, you can look at this thread for a discussion on this topic: