Pipeline configuration

This page includes links to everything needed to get started with the pipeline system.

The system’s front end, xcpEngine, accepts two primary arguments: a design file and a cohort file.

• The design file parameterizes the processing streams and specifies the Modules that should be run.
• The cohort file is a list of subjects; it defines the inputs to the pipeline.

• Pipeline tutorial
  • 0. Before you begin
  • 1. Running the anatomical pipeline
  • 2. Running a functional connectivity pipeline
  • 3. Running a ASL processing pipeline
  • 4. Arguments
  • 5. Output files
  • 6. Anatomy of the pipeline system
  • 7. Getting help
  • 8. Common Errors
• Pipeline design file
  • Preparing the design file
• Pipeline cohort file
  • Examples
  • Subject variables
• xcpEngine
  • -d: Design file
  • -c: Cohort file
  • -o: Output path
  • -i: Intermediate path
  • -r: Reference directory
  • -a: Direct assignment
  • -t: Trace (verbosity) level
• Processing streams
  • Anatomical processing streams
  • Functional connectivity streams
  • Arterial spin labeling streams