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BIDS in R – (it’s a start!)
The goal of bidser is to make working with the BIDS neuroimaging format convenient in R. Current support is strongest for MRI datasets, with explicit query helpers, metadata inheritance, derivative pipeline discovery, and compatibility-oriented support for fmriprep workflows.
Install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("bbuchsbaum/bidser")See https://bbuchsbaum.github.io/bidser/articles/quickstart.html
read_confounds() selects nuisance regressors from
fMRIPrep confound tables. Rather than hand-listing version-specific
column names, use the high-level, version-robust helpers:
# Named, version-robust sets (resolve to whatever columns your dataset has)
read_confounds(proj, cvars = confound_set("motion24"))
read_confounds(proj, cvars = confound_set("36p"))
# PCA + raw denoising strategies (recommended modern default)
read_confounds(proj, cvars = confound_strategy("pcabasic80"))
# Discover what is available
list_confound_sets()
list_confound_strategies()Code that previously reached into the unexported
bidser:::DEFAULT_CVARS2 should switch to the stable public
handle confound_set("legacy_default"), which returns the
identical 26-name set. See ?read_confounds,
?confound_set, and the confounds-and-variables
vignette for details.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.