The .cbrain folder in Processing Outputs

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.