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.
- 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_atlasschema. - 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.
# Install from GitHub (development version)
# install.packages("pak")
pak::pak("circadia-bio/boldR")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 |
- Lucas França — Circadia Lab, Northumbria University
- Mario Leocadio-Miguel — Circadia Lab, Northumbria University
MIT © 2026 Lucas França, Mario Leocadio-Miguel