cpac (Python package)

cpac is available so that you can easily run analyses without needing interact with the container platform that allows you to run C-PAC without installing all of the underlying software.

cpac requires Python 3.6 or greater. To get cpac, simply

pip install cpac

Download / Upgrade C-PAC with cpac

To download or upgrade a particular C-PAC image,

cpac pull

or

cpac upgrade

When downloading/upgrading, the --platform, --image, and --tag let you specify platform (Docker or Singularity), image (Docker image name or URL to image in repository), and tag (version tag, currently only for Docker repositories), respectively.

For example, a development Docker image can be downloaded with

cpac --platform docker --tag nightly pull

Or a Singularity image built from that Docker image can be downloaded with

cpac --platform singularity --tag nightly pull

Run C-PAC with cpac

To run C-PAC in participant mode for one participant, using a BIDS dataset stored on your machine or server and using the container image’s default pipeline configuration:

cpac run /Users/You/local_bids_data /Users/You/some_folder_for_outputs participant

By default, cpac (the wrapper) will try Docker first and fall back to Singularity if Docker fails. If both fail, an exception is raised.

You can specify a platform with the --platform docker or --platform singularity. If you specify a platform without specifying an image, these are the defaults, using the first successfully found image:

Usage

$ cpac --help

usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
            [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
            [--working_dir PATH] [-v] [-vv]
            {run,utils,version,group,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
            ...

cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images.

This commandline interface package is designed to minimize repetition.
As such, nearly all arguments are optional.

When launching a container, this package will try to bind any paths mentioned in
 • the command
 • the data configuration

An example minimal run command:
     cpac run /path/to/data /path/for/outputs

An example run command with optional arguments:
     cpac -B /path/to/data/configs:/configs \
             --image fcpindi/c-pac --tag latest \
             run /path/to/data /path/for/outputs \
             --data_config_file /configs/data_config.yml \
             --save_working_dir

Each command can take "--help" to provide additonal usage information, e.g.,

     cpac run --help

Known issues:
- Some Docker containers unexpectedly persist after cpac finishes. To clear them, run
    1. `docker ps` to list the containers
  For each C-PAC conatainer that persists, run
    2. `docker attach <container_name>`
    3. `exit`
- https://github.com/FCP-INDI/cpac/issues

positional arguments:
  {run,utils,version,group,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
    run                 Run C-PAC. See
                        "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] run --help"
                        for more information.
    utils               Run C-PAC commandline utilities. See
                        "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] utils --help"
                        for more information.
    version             Print the version of C-PAC that cpac is using.
    group               Run a group level analysis in C-PAC. See
                        "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] group --help"
                        for more information.
    pull (upgrade)      Upgrade your local C-PAC version to the latest version
                        by pulling from Docker Hub or other repository.
                        Use with "--image" and/or "--tag" to specify an image
                        other than the default "fcpindi/c-pac:latest" to pull.
    enter (bash, shell)
                        Enter a new C-PAC container via BASH.
    parse-resources (parse_resources)
                        When provided with a `callback.log` file, this utility can sort through
                        the memory `runtime` usage, `estimate`, and associated `efficiency`, to
                        identify the `n` tasks with the `highest` or `lowest` of each of these
                        categories.
                        "parse-resources" is intended to be run outside a C-PAC container.
                        See "cpac parse-resources --help" for more information.
    crash               Convert a crash pickle to plain text (C-PAC < 1.8.0).

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  -o OPT, --container_option OPT
                        parameters and flags to pass through to Docker or Singularity

                        This flag can take multiple arguments so cannot be
                        the final argument before the command argument (i.e.,
                        run or any other command that does not start with - or --)
  -B CUSTOM_BINDING, --custom_binding CUSTOM_BINDING
                        directories to bind with a different path in
                        the container than the real path of the directory.
                        One or more pairs in the format:
                             real_path:container_path
                        (eg, /home/C-PAC/run5/outputs:/outputs).
                        Use absolute paths for both paths.

                        This flag can take multiple arguments so cannot be
                        the final argument before the command argument (i.e.,
                        run or any other command that does not start with - or --)
  --platform {docker,singularity}
                        If neither platform nor image is specified,
                        cpac will try Docker first, then try
                        Singularity if Docker fails.
  --image IMAGE         path to Singularity image file OR name of Docker image (eg, "fcpindi/c-pac").
                        Will attempt to pull from Singularity Hub or Docker Hub if not provided.
                        If image is specified but platform is not, platform is
                        assumed to be Singularity if image is a path or
                        Docker if image is an image name.
  --tag TAG             tag of the Docker image to use (eg, "latest" or "nightly").
  --working_dir PATH    working directory
  -v, --verbose         set loglevel to INFO
  -vv, --very-verbose   set loglevel to DEBUG

--platform docker

  • Look for fcpindi/c-pac:latest locally.

  • Pull fcpindi/c-pac:latest from Docker Hub.

--platform singularity

  • Look in the present working directory for any Singularity images. If more than one is found, use the most recently modified.

  • Pull FCP-INDI/C-PAC from Singularity Hub.

  • Pull fcpindi/c-pac:latest from Docker Hub and convert to a Singularity image.

You can also specify a container image with an --image argument, passing an image name (e.g., fcpindi/c-pac) for a Docker image or a filepath (e.g. ~/singularity_images/C-PAC.sif) for a Singularity image. You can also specify a --tag (e.g., latest or nightly).

You can also provide a link to an AWS S3 bucket containing a BIDS directory as the data source:

cpac run s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS /Users/You/some_folder_for_outputs participant

In addition to the default pipeline, C-PAC comes packaged with a growing library of pre-configured pipelines that are ready to use. To run C-PAC with one of the pre-packaged pre-configured pipelines, simply invoke the --preconfig flag, shown below. See the full selection of pre-configured pipelines here.

cpac run /Users/You/local_bids_data /Users/You/some_folder_for_outputs --preconfig anat-only

To run C-PAC with a pipeline configuration file other than one of the pre-configured pipelines, assuming the configuration file is in the /Users/You/Documents directory:

cpac run /Users/You/local_bids_data /Users/You/some_folder_for_outputs participant --pipeline_file /Users/You/Documents/pipeline_config.yml

Finally, to run C-PAC with a specific data configuration file (instead of providing a BIDS data directory):

cpac run /Users/You/any_directory /Users/You/some_folder_for_outputs participant --data_config_file /Users/You/Documents/data_config.yml

Note: we are still providing the postionally-required bids_dir input parameter. However C-PAC will not look for data in this directory when you provide a data configuration YAML with the --data_config_file flag. Providing . or $PWD will simply pass the present working directory. In addition, if the dataset in your data configuration file is not in BIDS format, just make sure to add the --skip_bids_validator flag at the end of your command to bypass the BIDS validation process.

The full list of parameters and options that can be passed to C-PAC are shown below:

Usage: cpac run

$ cpac run --help

Loading 🐳 Docker
Could not create /output. Binding /output to /home/circleci/build/output instead.
Could not create /logs. Binding /logs to /home/circleci/build/logs instead.
Could not create /crash. Binding /crash to /home/circleci/build/crash instead.
Loading 🐳 fcpindi/c-pac:latest as "circleci (3434)" with these directory bindings:
  local                        Docker                mode
  ---------------------------  --------------------  ------
  /etc/passwd                  /etc/passwd           ro
  /home/circleci/.cpac         /home/circleci/.cpac  rw
  /home/circleci/build         /home/circleci/build  rw
  /tmp                         /tmp                  rw
  /home/circleci/build/output  /output               rw
  /home/circleci/build/logs    /logs                 rw
  /home/circleci/build/crash   /crash                rw
Logging messages will refer to the Docker paths.

usage: run.py [-h] [--pipeline_file PIPELINE_FILE] [--group_file GROUP_FILE]
              [--data_config_file DATA_CONFIG_FILE] [--preconfig PRECONFIG]
              [--aws_input_creds AWS_INPUT_CREDS]
              [--aws_output_creds AWS_OUTPUT_CREDS] [--n_cpus N_CPUS]
              [--mem_mb MEM_MB] [--mem_gb MEM_GB]
              [--num_ants_threads NUM_ANTS_THREADS]
              [--random_seed RANDOM_SEED]
              [--save_working_dir [SAVE_WORKING_DIR]] [--disable_file_logging]
              [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
              [--participant_ndx PARTICIPANT_NDX] [--T1w_label T1W_LABEL]
              [--bold_label BOLD_LABEL [BOLD_LABEL ...]] [-v]
              [--bids_validator_config BIDS_VALIDATOR_CONFIG]
              [--skip_bids_validator] [--anat_only] [--tracking_opt-out]
              [--monitoring]
              bids_dir output_dir {participant,group,test_config,cli}

C-PAC Pipeline Runner

positional arguments:
  bids_dir              The directory with the input dataset formatted
                        according to the BIDS standard. Use the format
                        s3://bucket/path/to/bidsdir to read data directly from
                        an S3 bucket. This may require AWS S3 credentials
                        specified via the --aws_input_creds option.
  output_dir            The directory where the output files should be stored.
                        If you are running group level analysis this folder
                        should be prepopulated with the results of the
                        participant level analysis. Use the format
                        s3://bucket/path/to/bidsdir to write data directly to
                        an S3 bucket. This may require AWS S3 credentials
                        specified via the --aws_output_creds option.
  {participant,group,test_config,cli}
                        Level of the analysis that will be performed. Multiple
                        participant level analyses can be run independently
                        (in parallel) using the same output_dir. test_config
                        will run through the entire configuration process but
                        will not execute the pipeline.

optional arguments:
  -h, --help            show this help message and exit
  --pipeline_file PIPELINE_FILE
                        Path for the pipeline configuration file to use. Use
                        the format s3://bucket/path/to/pipeline_file to read
                        data directly from an S3 bucket. This may require AWS
                        S3 credentials specified via the --aws_input_creds
                        option.
  --group_file GROUP_FILE
                        Path for the group analysis configuration file to use.
                        Use the format s3://bucket/path/to/pipeline_file to
                        read data directly from an S3 bucket. This may require
                        AWS S3 credentials specified via the --aws_input_creds
                        option. The output directory needs to refer to the
                        output of a preprocessing individual pipeline.
  --data_config_file DATA_CONFIG_FILE
                        Yaml file containing the location of the data that is
                        to be processed. This file is not necessary if the
                        data in bids_dir is organized according to the BIDS
                        format. This enables support for legacy data
                        organization and cloud based storage. A bids_dir must
                        still be specified when using this option, but its
                        value will be ignored. Use the format
                        s3://bucket/path/to/data_config_file to read data
                        directly from an S3 bucket. This may require AWS S3
                        credentials specified via the --aws_input_creds
                        option.
  --preconfig PRECONFIG
                        Name of the pre-configured pipeline to run.
  --aws_input_creds AWS_INPUT_CREDS
                        Credentials for reading from S3. If not provided and
                        s3 paths are specified in the data config we will try
                        to access the bucket anonymously use the string "env"
                        to indicate that input credentials should read from
                        the environment. (E.g. when using AWS iam roles).
  --aws_output_creds AWS_OUTPUT_CREDS
                        Credentials for writing to S3. If not provided and s3
                        paths are specified in the output directory we will
                        try to access the bucket anonymously use the string
                        "env" to indicate that output credentials should read
                        from the environment. (E.g. when using AWS iam roles).
  --n_cpus N_CPUS       Number of execution resources per participant
                        available for the pipeline. This flag takes precidence
                        over max_cores_per_participant in the pipeline
                        configuration file.
  --mem_mb MEM_MB       Amount of RAM available per participant in megabytes.
                        Included for compatibility with BIDS-Apps standard,
                        but mem_gb is preferred. This flag takes precedence
                        over maximum_memory_per_participant in the pipeline
                        configuration file.
  --mem_gb MEM_GB       Amount of RAM available per participant in gigabytes.
                        If this is specified along with mem_mb, this flag will
                        take precedence. This flag also takes precedence over
                        maximum_memory_per_participant in the pipeline
                        configuration file.
  --num_ants_threads NUM_ANTS_THREADS
                        The number of cores to allocate to ANTS-based
                        anatomical registration per participant. Multiple
                        cores can greatly speed up this preprocessing step.
                        This number cannot be greater than the number of cores
                        per participant.
  --random_seed RANDOM_SEED
                        Random seed used to fix the state of execution. If
                        unset, each process uses its own default. If set, a
                        `random.log` file will be generated logging the random
                        state used by each process. If set to a positive
                        integer (up to 2147483647), that integer will be used
                        to seed each process. If set to 'random', a random
                        seed will be generated and recorded for each process.
  --save_working_dir [SAVE_WORKING_DIR]
                        Save the contents of the working directory.
  --disable_file_logging
                        Disable file logging, this is useful for clusters that
                        have disabled file locking.
  --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        The label of the participant that should be analyzed.
                        The label corresponds to sub-<participant_label> from
                        the BIDS spec (so it does not include "sub-"). If this
                        parameter is not provided all participants should be
                        analyzed. Multiple participants can be specified with
                        a space separated list.
  --participant_ndx PARTICIPANT_NDX
                        The index of the participant that should be analyzed.
                        This corresponds to the index of the participant in
                        the data config file. This was added to make it easier
                        to accommodate SGE array jobs. Only a single
                        participant will be analyzed. Can be used with
                        participant label, in which case it is the index into
                        the list that follows the participant_label flag. Use
                        the value "-1" to indicate that the participant index
                        should be read from the AWS_BATCH_JOB_ARRAY_INDEX
                        environment variable.
  --T1w_label T1W_LABEL
                        C-PAC only runs one T1w per participant-session at a
                        time, at this time. Use this flag to specify any BIDS
                        entity (e.g., "acq-VNavNorm") or sequence of BIDS
                        entities (e.g., "acq-VNavNorm_run-1") to specify which
                        of multiple T1w files to use. Specify "--T1w_label
                        T1w" to choose the T1w file with the fewest BIDS
                        entities (i.e., the final option of [*_acq-
                        VNavNorm_T1w.nii.gz, *_acq-HCP_T1w.nii.gz,
                        *_T1w.nii.gz"]). C-PAC will choose the first T1w it
                        finds if the user does not provide this flag, or if
                        multiple T1w files match the --T1w_label provided. If
                        multiple T2w files are present and a comparable filter
                        is possible, T2w files will be filtered as well. If no
                        T2w files match this --T1w_label, T2w files will be
                        processed as if no --T1w_label were provided.
  --bold_label BOLD_LABEL [BOLD_LABEL ...]
                        To include a specified subset of available BOLD files,
                        use this flag to specify any BIDS entity (e.g., "task-
                        rest") or sequence of BIDS entities (e.g. "task-
                        rest_run-1"). To specify the bold file with the fewest
                        BIDS entities in the file name, specify "--bold_label
                        bold". Multiple `--bold_label`s can be specified with
                        a space-separated list. If multiple `--bold_label`s
                        are provided (e.g., "--bold_label task-rest_run-1
                        task-rest_run-2", each scan that includes all BIDS
                        entities specified in any of the provided
                        `--bold_label`s will be analyzed. If this parameter is
                        not provided all BOLD scans should be analyzed.
  -v, --version         show program's version number and exit
  --bids_validator_config BIDS_VALIDATOR_CONFIG
                        JSON file specifying configuration of bids-validator:
                        See https://github.com/bids-standard/bids-validator
                        for more info.
  --skip_bids_validator
                        Skips bids validation.
  --anat_only           run only the anatomical preprocessing
  --tracking_opt-out    Disable usage tracking. Only the number of
                        participants on the analysis is tracked.
  --monitoring          Enable monitoring server on port 8080. You need to
                        bind the port using the Docker flag "-p".

Usage: cpac utils

$ cpac utils --help

Loading 🐳 Docker
Could not create /crash. Binding /crash to /home/circleci/build/crash instead.
Could not create /logs. Binding /logs to /home/circleci/build/logs instead.
Could not create /output. Binding /output to /home/circleci/build/output instead.
Loading 🐳 fcpindi/c-pac:latest as "circleci (3434)" with these directory bindings:
  local                        Docker                mode
  ---------------------------  --------------------  ------
  /etc/passwd                  /etc/passwd           ro
  /home/circleci/.cpac         /home/circleci/.cpac  rw
  /home/circleci/build         /home/circleci/build  rw
  /home/circleci/build/crash   /crash                rw
  /tmp                         /tmp                  rw
  /home/circleci/build/logs    /logs                 rw
  /home/circleci/build/output  /output               rw
Logging messages will refer to the Docker paths.

Usage: run.py utils [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  crash
  data_config
  group_config
  pipe_config
  repickle
  test
  tools
  workflows

Note that any of the optional arguments above will over-ride any pipeline settings in the default pipeline or in the pipeline configuration file you provide via the --pipeline_file parameter.

Further usage notes:

  • You can run only anatomical preprocessing easily, without modifying your data or pipeline configuration files, by providing the --anat_only flag.

  • As stated, the default behavior is to read data that is organized in the BIDS format. This includes data that is in Amazon AWS S3 by using the format s3://<bucket_name>/<bids_dir> for the bids_dir command line argument. Outputs can be written to S3 using the same format for the output_dir. Credentials for accessing these buckets can be specified on the command line (using --aws_input_creds or --aws_output_creds).

  • When the app is run, a data configuration file is written to the working directory. This directory can be specified with --working_dir or the directory from which you run cpac will be used. This file can be passed into subsequent runs, which avoids the overhead of re-parsing the BIDS input directory on each run (i.e. for cluster or cloud runs). These files can be generated without executing the C-PAC pipeline using the test_run command line argument.

  • The participant_label and participant_ndx arguments allow the user to specify which of the many datasets should be processed, which is useful when parallelizing the run of multiple participants.

  • If you want to pass runtime options to your container plaform (Docker or Singularity), you can pass them with -o or --container_options.

Footnotes

*

The version restrictions for Singularity are specific to cpac the convenience wrapper. C-PAC itself should run on Singularity 2 or 3.