Lack of Skull Stripping in fMRIPrep Output for Coregistration

Software Support
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Hi everyone,

I have a specific question regarding the fMRIPrep output, particularly in the section for “Alignment of functional and anatomical MRI data (coregistration).” I noticed that both my T1W and BOLD images are not skull stripped (as shown in the image below).

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I plan to use AFNI for smoothing, scaling, and further analysis. What impact will it have if the skull is not removed? According to the fMRIPrep instruction document, isn’t skull stripping supposed to be done automatically?

Thank you very much for your assistance!

Best,
Shuning