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-

Hi,

I ran into the same issue a few days ago (see: https://www.nitrc.org/forum/forum.php?thread_id=15985&forum_id=1144 )

I’m still having trouble fully understanding it and haven’t found a solution yet. In the meantime, could you let me know whether you were able to complete the analysis? If so, did you try overlaying the denoised functional image (dswau*.nii) onto the anatomical image (wc0c*.nii)? In my case, they never align (see Figure 1). Interestingly, the smoothed but non-denoised images (swau*.nii) consistently align perfectly with the anatomical image (see Figure 2).

FIGURE 1:

FIGURE 2:

Kind regards,

Adrian.