Run the processing pipeline

Usage

run_project(
  scfg,
  steps = NULL,
  subject_filter = NULL,
  postprocess_streams = NULL,
  extract_streams = NULL,
  debug = FALSE,
  force = FALSE
)

Arguments

scfg: a project configuration object as produced by load_project or setup_project
steps: Character vector of pipeline steps to execute (or "all" to run all steps). Options are c("flywheel_sync", "bids_conversion", "mriqc", "fmriprep", "aroma", "postprocess", "extract_rois"). If NULL, the user will be prompted for which steps to run.
subject_filter: Optional character vector or data.frame specifying which subjects (and optionally sessions) to process. When NULL and run interactively, the user will be prompted to enter space-separated subject IDs (press ENTER to process all subjects). When a data.frame is provided, it must contain a sub_id column and may include a ses_id column to filter on specific subject/session combinations.
postprocess_streams: Optional character vector specifying which postprocessing streams should be run. If "postprocess"`` is included in steps`, then this setting lets the user choose streams. If NULL, all postprocess streams will be run.
extract_streams: Optional character vector specifying which ROI extraction streams should be run. If "extract_rois"`` is included in steps`, then this setting lets the user choose streams. If NULL, all extraction streams will be run.
debug: A logical value indicating whether to run in debug mode (verbose output for debugging, no true processing).
force: A logical value indicating whether to force the execution of all steps, regardless of their current status.

Value

A logical value indicating whether the processing pipeline was successfully run.

Examples

  if (FALSE) { # \dontrun{
    # Assuming you have a valid project configuration list named `study_config`
    run_project(study_config, prompt = TRUE, force = FALSE)
  } # }