Running C-PAC


As with configuring the subject list, pipeline configuration, and group analysis files, there are two ways of executing a C-PAC run:

  • Using C-PAC’s command line interface
  • Using the main dialog in the C-PAC GUI

This page will also discuss how to navigate C-PAC’s output structure once a run is finished.

Using the Command Line Interface

Running Preprocessing and Individual-Level Analysis

To start a C-PAC run from the command line or a shell script you can use the utility (which is added to your path automatically upon installing C-PAC). An example of this tool’s syntax is as follows: /path/to/pipeline_config.yml /path/to/CPAC_subject_list.yml

Using the GUI

Running Preprocessing and Individual-Level Analysis

You have already interacted with the Subject Lists and Pipelines panes in the main dialog in order to create new subject lists and pipeline configurations. There is, however, more to the main dialog than making new files! Both panes have a Load option that will load in any previously created YAML files. Additionally, there is a View button that allows you to inspect the text of the YAML files for the currently selected subject list or pipeline configuration and a Clear button that removes all loaded pipelines or subject lists. The Pipelines pane sports an Edit button that allows you to modify already loaded pipeline configurations, as well as options for renaming and deleting pipeline configurations.

If you have loaded multiple subject lists or pipeline configurations, click the checkboxes to the left of the subject list names in the Subject Lists pane to select which sets of subjects you would like to run. Similarly, select the pipelines you’d like to run in the adjacent Pipelines pane. When you are ready to run C-PAC, click the Run Individual Level Analysis button at the bottom.

Note: Do not confuse the *Load* button on the main window of the GUI with the *Load Settings* button within the Subject List Setup window shown above. The latter button is intended to load data configuration files that the subject list setup dialogue can use to create subject lists and will not work with other YAML files. The former button is for already generated subject list files.


The following schematic illustrates the order in which C-PAC executes.


Running Group-Level Analysis

When you are ready to run group-level analysis, select the subject lists and pipelines you would like to run and click the Run Group Level Analysis button. You will be presented with a dialog and asked to select which strategies you would like to include.

Output Structure

File Descriptions

Preprocessed anatomical data from the Anatomical Preprocessing, Registration, and Segmentation workflows can be found in ../scan/anat/ directory for each subject. The following diagram shows processing steps and standard output files for these workflows.


Preprocessed functional data from the Functional Preprocessing workflow can be found in the ../scan_<name>/func directory for each subject. The following diagram shows processing steps and standard output files for this workflow.


Derivative Outputs

Derivatives for each subject can be found in the ../scan_<name> directory of each subject. This folder also contains the outputs of the registration and segmentation workflows.


Within each derivative folder will be sub-folders for each set of frequency filters set in config.yml, as well as a folder containing smoothed outputs.

Derivatives are output in both native space (*_img.nii.gz and *_map.nii.gz files), with values transformed to z-scores (*_Z_*.nii.gz) and in standard space (*_to_standard.nii.gz).