Dear Dr. Alfonso and the CONN community,

I am currently analyzing resting-state fMRI data for 12 PPMI subjects using the default preprocessing pipeline in the latest version of CONN.

While reviewing the Denoising tab, I noticed that the functional brain mask (BOLD %) does not align correctly with the anatomical image for 2 subjects. One of them is a subject already excluded due to severe motion, which I can understand. However, the other one (Subject 3) was not excluded, yet still shows a severe misalignment (please see the attached image).

I found some forum posts mentioning this might be a centering or normalization issue. However, I ran the default preprocessing pipeline, which I believe already includes automatic centering. Furthermore, when I checked the 2nd-level QA covariates related to normalization, Subject 3 did not seem to show any obvious outlier flags.

Could you please advise why this misalignment occurred despite using the default pipeline? Is there a specific QA metric I am missing that should have caught this, and how can I manually fix this specific subject?

I have attached a single screenshot showing the misaligned brain map for your reference.

Thank you

-minsu kim-