# Bayesian Uncertainty Quantification for fMRI Functional Connectivity via Simulation-Based Inference

arXiv: https://arxiv.org/abs/2609.30445 · HTML: https://mlsanity.com/paper/2609.30445/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 58 references that are in the map.
- First posted on arXiv 24 Sep 2026.

## Builds on (most cited first, 8 of 8)

- [Normalizing Flows for Probabilistic Modeling and Inference](https://mlsanity.com/paper/1912.02762/) (2019)
- [The frontier of simulation-based inference](https://mlsanity.com/paper/1911.01429/) (2019)
- [Benchmarking Simulation-Based Inference](https://mlsanity.com/paper/2101.04653/) (2021)
- [Validating Bayesian Inference Algorithms with Simulation-Based Calibration](https://mlsanity.com/paper/1804.06788/) (2018)
- [Machine Learning for Neuroimaging with Scikit-Learn](https://mlsanity.com/paper/1412.3919/) (2014)
- [A Trust Crisis In Simulation-Based Inference? Your Posterior Approximations Can Be Unfaithful](https://mlsanity.com/paper/2110.06581/) (2021)
- [Balancing Simulation-based Inference for Conservative Posteriors](https://mlsanity.com/paper/2304.10978/) (2023)
- [Parameter estimation from an Ornstein-Uhlenbeck process with measurement noise](https://mlsanity.com/paper/2305.13498/) (2023)

## Abstract (arXiv)

Optimizing fMRI scan duration and spatial resolution is critical for experimental design, yet traditional correlation-based approaches cannot quantify uncertainty or disentangle scanner measurement noise from true neural variability across subjects. Without principled uncertainty bounds, researchers cannot know whether a protocol is long enough to reliably estimate connectivity, or whether between-subject differences reflect biological variation or noise. We present a Bayesian framework modeling BOLD dynamics as coupled Ornstein-Uhlenbeck processes, using Sequential Neural Posterior Estimation to obtain connectivity posteriors while accounting for frequency-independent measurement noise across the BOLD spectrum. Applied to N = 28 healthy controls (55 scans) at 7T using a functional network atlas (65 DMN regions), the framework quantifies uncertainty across its sources: scanner noise, subject variability, and acquisition length. Spatial analysis identifies a mean of 46 voxels per ROI, roughly half of typical region sizes, as sufficient to achieve 90% of asymptotic precision. At the single-subject level, 7T reaches its within-session precision plateau in approximately 7 minutes versus 10 minutes for 3T, a 40% reduction in required scan time, providing the first direct, model-based quantification of the scan-time advantage conferred by higher field strength. At the population level, 3T requires roughly 37 times more per-subject scan time than 7T for the pooled curves to converge, confirming a consistent advantage of higher field strength at every timescale. Together these findings provide concrete, scanner-specific guidance for protocol optimization, with direct implications for reducing acquisition costs and improving the reliability of connectivity-based clinical biomarkers. We provide code enabling researchers to derive these bounds from their own data.