Dear CONN Toolbox Support Team,

I hope this message finds you well. I am reaching out regarding the preprocessing pipeline for an fMRI study I am conducting, for which we are utilizing the CONN toolbox to analyze functional connectivity. Our dataset was acquired using an interleaved slice acquisition method with a repetition time (TR) of 2.1 seconds. As we refine our preprocessing strategy, we seek your expertise to ensure the accuracy and effectiveness of our analysis.

Considering the interleaved acquisition and the specific TR of 2.1 seconds, we would like to inquire about the optimal sequencing of preprocessing steps, particularly the positioning of slice-timing correction (STC) in relation to coregistration. The guidance in the literature on this subject varies, and we aim to adopt the best practice as recommended for our specific scenario.

Our questions is as follows:

Given our data's TR of 2.1 seconds and interleaved acquisition pattern, is it recommended to perform STC before proceeding with head motion correction ('realignment and unwarp')? Or do you suggest to use the default preprocessing pipeline (head motion correction and then STC)?

We are committed to ensuring that our preprocessing pipeline is optimally configured for our study's unique requirements. Your advice and insights on this matter would be greatly appreciated.

Thank you very much for your support and for the invaluable resources provided by the CONN community. I look forward to your guidance.

Best regards,

Michelle