The .cbrain folder in Processing Outputs
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This page describes the .cbrain folder, which is found in many processing outputs
and contains detailed information about the processing that was performed.
For example, for a given set of pipeline outputs there is generally the following structure: ::
    
    pipeline_name/
    ├── sub-<label>/
    |   │   ├── ses-<label>/
    |   │   ├── .cbrain/
    |   │   │   │   ├── boutiques_descriptor.json
    |   │   │   │   ├── boutiques_invoke.json
    |   │   │   │   ├── cbrain_params.json
    |   │   │   │   ├── job_script.sh
    |   │   │   │   ├── runtime_info.properties
    |   │   │   │   ├── stderr.log
    |   │   │   │   ├── stdout.log
    │   │   ├── ... (other processing outputs)


Or alternatively: ::

    pipeline_name/
    ├── sub-<label>/
    |   │   ├── ses-<label>/
    │   ├── .cbrain/
    │   │   │   ├── boutiques_descriptor.json
    │   │   │   ├── boutiques_invoke.json
    │   │   │   ├── cbrain_params.json
    │   │   │   ├── job_script.sh
    │   │   │   ├── runtime_info.properties
    │   │   │   ├── stderr.log
    │   │   │   ├── stdout.log
    │   │   ├── ... (other processing outputs)

Within the files above, users are provided with the following information:

- The boutiques_descriptor.json file will contain the exact version of the boutiques descriptor that was used for processing.
- The boutiques_invoke.json will describe the arguments used for processing.
- The cbrain_params.json file will specify details including which files were used for processing.
  While this document does not contain the QC criteria that was used to include/exclude files from
  processing, it does contain the files that were chosen as a result of this process.
- The job_script.sh file has certain details about how CBRAIN configured processing on Minnesota Supercomputing Institute's
  cluster.
- The runtime_info.properties file will contain information about the processing script that was run.
- The stderr.log and stdout.log files will contain the standard error and standard output from the processing job.

.. note::
    If a pipeline output does not contain a ses-<label> folder, the .cbrain folder
    may be placed under the subject directory.