Subject: Follow-Up: Native-Space Processing & Regressors in CONN

Dear Alfonso,

Thank you again for your detailed guidance. I have one quick follow-up question based on your previous response and our current setup.

We are using externally preprocessed 7T fMRI data that has already undergone motion correction, slice timing correction, spatial smoothing, and coregistration—all performed outside of CONN. However, we noticed that CONN’s preprocessing pipeline also applies its own motion correction steps by default. This may result in redundant corrections.

Following our internal discussion (cc’d here), we are considering disabling CONN’s motion correction entirely and instead importing our own motion regressors through the first-level covariates tab. From your experience, would this be the appropriate approach for ensuring consistency with externally preprocessed native-space data?

Could you please confirm whether disabling CONN’s internal motion correction is necessary in our case, and whether this duplication of motion correction (from both our external preprocessing and CONN) could negatively impact the results?

Thank you again for your continued support!

Best regards,
Farzan Vahedifard