Read fMRIPrep BIDS derivatives for a participant

Reads preprocessed fMRI outputs from an fMRIPrep BIDS derivatives directory for a single participant and session, returning a structured boldR_fmriprep object containing paths to the BOLD, T1w, T2w, and segmentation files.

Usage

read_fmriprep(
  derivatives_dir,
  subject,
  session = NULL,
  task = NULL,
  space = "MNI152NLin2009cAsym",
  resolution = NULL
)

Arguments

derivatives_dir: Character. Path to the fMRIPrep derivatives root (e.g. "sub-01/func/"... or the top-level derivatives/fmriprep/).
subject: Character. Subject label without the sub- prefix (e.g. "01").
session: Character or NULL. Session label without the ses- prefix. If NULL (default), assumes a single-session dataset.
task: Character or NULL. Task label (e.g. "rest"). If NULL, the first task found is used.
space: Character. Template space for the BOLD and mask files. Default "MNI152NLin2009cAsym".
resolution: Character or NULL. Resolution label (e.g. "2"). If NULL, resolution is not filtered.

Value

A list of class boldR_fmriprep with components:

bold: Character. Path to the BOLD NIfTI file.
bold_mask: Character. Path to the brain mask NIfTI file.
t1w: Character. Path to the T1w NIfTI file in template space.
t2w: Character or NA. Path to the T2w NIfTI file if available.
dseg: Character. Path to the discrete segmentation NIfTI file.
confounds: Character. Path to the confounds TSV file.
subject: Character. Subject label.
session: Character or NA. Session label.
task: Character. Task label.
space: Character. Template space.
derivatives_dir: Character. Resolved path to the derivatives root.

Examples

if (FALSE) { # \dontrun{
fprep <- read_fmriprep(
  derivatives_dir = "data/derivatives/fmriprep",
  subject         = "01",
  task            = "rest"
)
fprep
} # }