Output Settings#

Working Directory - [path]: Directory where CPAC should store temporary and intermediate files. Path should not contain spaces.
Output Directory - [path]: Directory where CPAC should place processed data. This can also be an S3 bucket path prepended with ‘s3://’. Path should not contain spaces.
Log Directory - [path]: Directory where CPAC should place run logs. Path should not contain spaces.
Crash Log Directory - [path]: Directory where CPAC should write crash logs. Path should not contain spaces.
AWS Output Bucket Credentials (optional) - [path]: If setting the Output Directory to an S3 bucket, insert the path to your AWS credentials file here.,
S3 Encryption - [On, Off]: Enable server-side 256-AES encryption on data to the S3 bucket,
Write Extra Functional Outputs - [On, Off]: Include extra versions and intermediate steps of functional preprocessing in the output directory.
Write Debugging Outputs - [On, Off]: Include extra outputs in the output directory that may be of interest when more information about intermediate steps is needed.
Enable logging - [On, Off]: Whether to write log details of the pipeline. run to the logging files..
Remove Working Directory [On, Off]: Deletes the contents of the Working Directory after running. This saves disk space, but any additional preprocessing or analysis will have to be completely re-run.)
Create organized output directory - [On, Off]: Create a simplified version of the output directory.
Regenerate Outputs - [On, Off]: Uses the contents of the working directory to regenerate all outputs and their symbolic links. Requires an intact working directory from a previous C-PAC run.
Enable Quality Control Interface - [On, Off]: Generate quality control pages containing preprocessing and derivative outputs.

Configuration Without the GUI#

The following nested key/value pairs will be set to these defaults if not defined in your pipeline configuration YAML.

pipeline_setup:

  # Name for this pipeline configuration - useful for identification.
  # This string will be sanitized and used in filepaths
  pipeline_name: cpac-default-pipeline

  output_directory:

    # Directory where C-PAC should write out processed data, logs, and crash reports.
    # - If running in a container (Singularity/Docker), you can simply set this to an arbitrary
    #   name like '/outputs', and then map (-B/-v) your desired output directory to that label.
    # - If running outside a container, this should be a full path to a directory.
    path: /outputs/output

    # (Optional) Path to a BIDS-Derivatives directory that already has outputs.
    #   - This option is intended to ingress already-existing resources from an output
    #     directory without writing new outputs back into the same directory.
    #   - If provided, C-PAC will ingress the already-computed outputs from this directory and
    #     continue the pipeline from where they leave off.
    #   - If left as 'None', C-PAC will ingress any already-computed outputs from the
    #     output directory you provide above in 'path' instead, the default behavior.
    source_outputs_dir: None

    # Set to True to make C-PAC ingress the outputs from the primary output directory if they
    # exist, even if a source_outputs_dir is provided
    #   - Setting to False will pull from source_outputs_dir every time, over-writing any
    #     calculated outputs in the main output directory
    #   - C-PAC will still pull from source_outputs_dir if the main output directory is
    #     empty, however
    pull_source_once: True

    # Include extra versions and intermediate steps of functional preprocessing in the output directory.
    write_func_outputs: False

    # Include extra outputs in the output directory that may be of interest when more information is needed.
    write_debugging_outputs: False

    # Output directory format and structure.
    # Options: default, ndmg
    output_tree: "default"

    # Quality control outputs
    quality_control:
      # Generate quality control pages containing preprocessing and derivative outputs.
      generate_quality_control_images: True

      # Generate eXtensible Connectivity Pipeline-style quality control files
      generate_xcpqc_files: False

  working_directory:

    # Directory where C-PAC should store temporary and intermediate files.
    # - This directory must be saved if you wish to re-run your pipeline from where you left off (if not completed).
    # - NOTE: As it stores all intermediate files, this directory can grow to become very
    #   large, especially for data with a large amount of TRs.
    # - If running in a container (Singularity/Docker), you can simply set this to an arbitrary
    #   name like '/work', and then map (-B/-v) your desired output directory to that label.
    # - If running outside a container, this should be a full path to a directory.
    # - This can be written to '/tmp' if you do not intend to save your working directory.
    path: /outputs/working

    # Deletes the contents of the Working Directory after running.
    # This saves disk space, but any additional preprocessing or analysis will have to be completely re-run.
    remove_working_dir: True

  log_directory:

    # Whether to write log details of the pipeline run to the logging files.
    run_logging: True

    path: /outputs/logs

    # Configuration options for logging visualizations of the workflow graph
    graphviz:
      # Configuration for a graphviz visualization of the entire workflow. See https://fcp-indi.github.io/docs/developer/nodes#CPAC.pipeline.nipype_pipeline_engine.Workflow.write_graph for details about the various options
      entire_workflow:
        # Whether to generate the graph visualization
        generate: Off
        # Options: [orig, hierarchical, flat, exec, colored]
        graph2use: []
        # Options: [svg, png]
        format: []
        # The node name will be displayed in the form `nodename (package)` when On or `nodename.Class.package` when Off
        simple_form: On

  crash_log_directory:

    # Directory where CPAC should write crash logs.
    path: /outputs/crash

  Amazon-AWS:

    # If setting the 'Output Directory' to an S3 bucket, insert the path to your AWS credentials file here.
    aws_output_bucket_credentials:

    # Enable server-side 256-AES encryption on data to the S3 bucket
    s3_encryption: False

  Debugging:

    # Verbose developer messages.
    verbose: Off