1 2 3 Intrinsic Functional Connectivity As a Tool For Human Connectomics : 4 Theory , Properties , and Optimization 5 6 7

33 34 Resting state functional connectivity MRI (fcMRI) is widely used to investigate 35 brain networks that exhibit correlated fluctuations. While fcMRI does not provide direct 36 measurement of anatomic connectivity, accumulating evidence suggests it is sufficiently 37 constrained by anatomy to allow the architecture of distinct brain systems to be 38 characterized. fcMRI is particularly useful for characterizing large-scale systems that 39 span distributed areas (e.g., polysynaptic cortical pathways, cerebro-cerebellar circuits, 40 cortical-thalamic circuits) and has complementary strengths when contrasted with the 41 other major tool available for human connectomics – high angular resolution diffusion 42 imaging (HARDI). We review what is known about fcMRI and then explore fcMRI data 43 reliability, effects of preprocessing, analysis procedures, and effects of different 44 acquisition parameters across six studies (n=98) to provide recommendations for 45 optimization. Run length (2 to 12 min), run structure (one 12-min run or two 6-min runs), 46 temporal resolution (2.5 or 5.0 sec), spatial resolution (2 or 3 mm), and the task (fixation, 47 eyes closed rest, eyes open rest, continuous word-classification) were varied. Results 48 revealed moderate to high test-retest reliability. Run structure, temporal resolution, and 49 spatial resolution minimally influenced fcMRI results while fixation and eyes open rest 50 yielded stronger correlations as contrasted to other task conditions. Commonly used 51 preprocessing steps involving regression of nuisance signals minimized non-specific 52 (noise) correlations including those associated with respiration. The most surprising 53 finding was that estimates of correlation strengths stabilized with acquisition times as 54 brief as 5 min. The brevity and robustness of fcMRI positions it as a powerful tool for 55 large-scale explorations of genetic influences on brain architecture. We conclude by 56 discussing the strengths and limitations of fcMRI and how it can be combined with 57 HARDI techniques to support the emerging field of human connectomics. 58 59 60 61