🧠 boldR

fmriprep gets you clean data. boldR gets you useful data.

⚠️ boldR is in early development and has not been formally tested. The API may change without notice, estimation results have not yet been validated against a reference implementation, and the package has not undergone peer review. Use with caution and verify outputs independently before using in any research context.

boldR is an R package for analysing Blood-Oxygen-Level-Dependent (BOLD) fMRI data in the context of sleep and circadian research. It picks up exactly where fMRIPrep leaves off — working directly with preprocessed BIDS derivatives — and transforms them into analysis-ready outputs.

boldR is part of the Circadia Lab R ecosystem at Northumbria University.

Key features

fMRIPrep as the input standard — reads preprocessed BIDS derivatives directly; no custom preprocessing required.
Atlas-agnostic parcellation — built-in support for common atlases (Schaefer, AAL); custom atlases accepted via a simple boldR_atlas schema.
Voxelwise metrics — temporal SNR, voxelwise GLM contrasts.
ROI-level outputs — timeseries extraction, functional connectivity matrices, summary metrics per ROI.
syncR-ready export — parcellated BOLD data flows directly into syncR::sync() alongside actigraphy, PSG, and questionnaire data.

Installation

# Install from GitHub (development version)
# install.packages("pak")
# pak::pak("circadia-bio/boldR")
install.packages("boldR", repos = c('https://circadia-bio.r-universe.dev', 'https://cloud.r-project.org'))

Ecosystem

fmriprep → boldR ──────────────────→ syncR
                 └─→ (parcellated)

boldR is designed to be used alongside:

Package	Role
`zeitR`	Actigraphy & circadian metrics
`mrpheus`	PSG signal analysis
`hypnor`	Hypnogram handling & sleep architecture
`slumbR`	Sleep diary processing
`syncR`	Unified participant database

Authors

Lucas França — Circadia Lab, Northumbria University
Mario Leocadio-Miguel — Circadia Lab, Northumbria University

🧠 boldR

Key features

Installation

Ecosystem

Authors

License