Locate fMRIPrep preprocessed files — ni_fmriprep

Searches for preprocessed files in an fMRIPrep derivatives directory and returns a data.frame with file paths and parsed BIDS entities.

Usage

ni_fmriprep_preproc(
  deriv_dir,
  subid = NULL,
  task = NULL,
  session = NULL,
  run = NULL,
  space = NULL,
  suffix = NULL,
  extension = ".nii.gz"
)

Arguments

deriv_dir: Path to the fMRIPrep derivatives directory.
subid: Subject ID (without "sub-" prefix). Default: NULL (all subjects).
task: Task name filter (without "task-" prefix). Default: NULL.
session: Session ID filter (without "ses-" prefix). Default: NULL.
run: Run number filter (without "run-" prefix). Default: NULL.
space: Space filter (without "space-" prefix, e.g. "MNI152NLin2009cAsym"). Default: NULL.
suffix: Suffix filter (e.g. "bold", "T1w", "mask"). Default: NULL.
extension: File extension filter. Default: ".nii.gz".

Value

A data.frame with columns: path, subject, session, task, run, space, desc, suffix, datatype.

Details

fMRIPrep outputs follow the pattern: {deriv_dir}/sub-{subid}/[ses-{session}/]{anat|func}/sub-{subid}_[entities]_{suffix}{ext}

Examples

if (FALSE) { # \dontrun{
# Find all preprocessed bold files
bold <- ni_fmriprep_preproc(
  deriv_dir = "derivatives/fmriprep",
  suffix = "bold"
)

# Find specific subject/task in MNI space
preproc <- ni_fmriprep_preproc(
  deriv_dir = "derivatives/fmriprep",
  subid = "01",
  task = "rest",
  space = "MNI152NLin2009cAsym"
)
} # }