Evaluation of the variations in functional connectivity between blip-up and blip-down phase encodings

Motivation: Neuroimaging studies require selecting a phase encoding direction, but its impact on results is uncertain. Goal(s): Develop a method to evaluate variations in the functional connectivity between blip-up and blip-down phase encodings. Approach: Blip-up and blip-down EPI images were alternately acquired during fMRI TRs. Functional connectivity was calculated separately for each phase encoding direction, enabling a comparative analysis in connectivity patterns. Results: Significant variations in functional connectivity between the two phase encodings were observed in the prefrontal and temporal lobes. These differences are likely attributed to signal loss and reduced tSNR, which are distributed unevenly across various brain regions. Impact: Our research evaluated the variations in functional connectivity between blip-up and blip-down phase encodings, offering a foundation for selecting the appropriate phase encoding direction in resting state fMRI.