Build a manifest from a BIDS project

Uses bidser to discover preprocessed BOLD scans, events, confounds, TR, and run lengths for each subject of a BIDS dataset, returning an fmri_manifest (a list of per-subject bindings) suitable for instantiate().

Usage

from_bids(
  proj,
  task,
  space = NULL,
  confounds = NULL,
  mask = NULL,
  desc = "preproc",
  subjects = NULL,
  ...
)

Arguments

proj

A bidser::bids_project (opened with fmriprep = TRUE for derivative discovery).

task

BIDS task label.

space

BIDS space for preprocessed scans (e.g. "MNI152NLin2009cAsym"); NULL matches any.

confounds

Confound selection passed to bidser::read_confounds() as cvars (character vector or a confound_set); NULL reads no confounds.

mask

A brain-mask path (length-1 character) applied to every subject's file-backed dataset. Required for file-backed BIDS data, which needs a mask (auto-resolution of the fmriprep brain mask is a planned enhancement).

desc

BIDS desc- label of the preprocessed scans (default "preproc").

subjects

Optional character vector of subject labels (bare ids, e.g. "01"); default is all participants.

...

Forwarded to bidser::read_confounds() (e.g. npcs, clean, na_action).

Value

An fmri_manifest: a list of bindings, one per subject.

Details

The design formula's variables must match the columns of the BIDS events.tsv (e.g. trial_type); a run column is added for the block structure. Confound columns are selected by confounds (a character vector or bidser::confound_set() result) passed straight to bidser::read_confounds().

See also

as_manifest(), instantiate(), preflight()

Examples

if (FALSE) { # \dontrun{
proj <- bidser::bids_project("study/", fmriprep = TRUE)
mani <- from_bids(proj, task = "stroop", space = "MNI152NLin2009cAsym",
                  confounds = bidser::confound_set("motion6"),
                  mask = "study/derivatives/.../space-MNI..._desc-brain_mask.nii.gz")
jobs <- instantiate(template, mani)
} # }