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🧠 boldR

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

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")

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

License

MIT © 2026 Lucas França, Mario Leocadio-Miguel