Installation | Basic workflow | 1. Read fMRIPrep derivatives | 2. Prepare the BOLD object | 3. Load an atlas and parcellate | Custom atlas | 4. Compute metrics | 5. Export for syncR | Ecosystem
Package: boldR 0.1.0
Lucas França
boldR: fMRI BOLD Signal Analysis for Circadian and Sleep Research
Analysis of Blood-Oxygen-Level-Dependent (BOLD) fMRI data for sleep and circadian research. Receives preprocessed derivatives from fMRIPrep and transforms them into analysis-ready outputs: atlas-agnostic parcellation with an extensible atlas schema, ROI-level timeseries extraction, voxelwise signal metrics (tSNR, GLM contrasts), and functional connectivity matrices. Exports parcellated BOLD data directly to syncR for integration with actigraphy, polysomnography, and questionnaire data in a unified participant-indexed database. Part of the Circadia Lab R ecosystem at Northumbria University. fmriprep gets you clean data. boldR gets you useful data.
Authors:
boldR_0.1.0.tar.gz
boldR_0.1.0.zip(r-4.7)boldR_0.1.0.zip(r-4.6)boldR_0.1.0.zip(r-4.5)
boldR_0.1.0.tgz(r-4.6-any)boldR_0.1.0.tgz(r-4.5-any)
boldR_0.1.0.tar.gz(r-4.7-any)boldR_0.1.0.tar.gz(r-4.6-any)
boldR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
boldR/json (API)
| # Install 'boldR' in R: |
| install.packages('boldR', repos = c('https://circadia-bio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/circadia-bio/boldr/issues
Pkgdown/docs site:https://boldr.circadia-lab.uk
Last updated from:0f58a3ab07 (on main). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 137 | ||
| source / vignettes | OK | 205 | ||
| linux-release-x86_64 | OK | 132 | ||
| macos-release-arm64 | OK | 131 | ||
| macos-oldrel-arm64 | OK | 123 | ||
| windows-devel | OK | 76 | ||
| windows-release | OK | 75 | ||
| windows-oldrel | OK | 72 | ||
| wasm-release | OK | 154 |
Exports:compute_fccompute_roi_metricscompute_tsnrexport_boldlist_atlasesload_atlaspalette_boldparcellateprepare_boldread_fmriprepregister_atlas
Dependencies:cligluelifecyclemagrittrpillarpkgconfigRcpprlangRNiftitibbleutf8vctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute functional connectivity from parcellated BOLD timeseries | compute_fc |
| Compute summary metrics per ROI | compute_roi_metrics |
| Compute voxelwise temporal SNR | compute_tsnr |
| Export parcellated BOLD data for syncR | export_bold |
| List available built-in atlases | list_atlases |
| Load a parcellation atlas | load_atlas |
| boldR colour palette | palette_bold |
| Extract ROI-level timeseries from a BOLD image | parcellate |
| Validate and prepare a fMRIPrep object for analysis | prepare_bold |
| Read fMRIPrep BIDS derivatives for a participant | read_fmriprep |
| Register a custom brain atlas | register_atlas |
