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Modern scientific discovery depends on collecting large heterogeneous datasets with many sources of variability, and applying domain-specific pipelines from which one can draw insight or clinical utility. For example, macroscale connectomics studies require complex pipelines to process raw functional or diffusion data and estimate connectomes. Individual studies tend to customize pipelines to their needs, raising concerns about their reproducibility, and adding to a longer list of factors that may differ across studies (including sampling, experimental design, and data acquisition protocols), resulting in failures to replicate. Mitigating these issues requires multi-study datasets and the development of pipelines that can be applied across them. We developed NeuroData's MRI to Graphs (NDMG) pipeline using several functional and diffusion studies, including the Consortium for Reliability and Reproducibility, to estimate connectomes. Without any manual intervention or parameter tuning, NDMG ran on 25 different studies (~6,000 scans) from 15 sites, with each scan resulting in a biologically plausible connectome (as assessed by multiple quality assurance metrics at each processing stage). For each study, the connectomes from NDMG are more similar within than across individuals, indicating that NDMG is preserving biological variability. Moreover, the connectomes exhibit near perfect consistency for certain connectional properties across every scan, individual, study, site, and modality; these include stronger ipsilateral than contralateral connections and stronger homotopic than heterotopic connections. Yet, the magnitude of the differences varied across individuals and studies - much more so when pooling data across sites, even after controlling for study, site, and basic demographic variables (i.e., age, sex, and ethnicity). This indicates that other experimental variables (possibly those not measured or reported) are contributing to this variability, which if not accounted for can limit the value of aggregate datasets, as well as expectations regarding the accuracy of findings and likelihood of replication. We, therefore, provide a set of principles to guide the development of pipelines capable of pooling data across studies while maintaining biological variability and minimizing measurement error. This open science approach provides us with an opportunity to understand and eventually mitigate spurious results for both past and future studies.

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