Usage: cpac runΒΆ

$ cpac run --help

Loading 🐳 Docker
Loading 🐳 fcpindi/c-pac:latest as "root (0)" with these directory bindings:
  local                         Docker                        mode
  ----------------------------  ----------------------------  ------
  /etc/passwd                   /etc/passwd                   ro
  /root/.cpac                   /root/.cpac                   rw
  /home/circleci/build          /home/circleci/build          rw
  /home/circleci/build/log      /home/circleci/build/log      rw
  /home/circleci/build/working  /home/circleci/build/working  rw
  /home/circleci/build/outputs  /home/circleci/build/outputs  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]
              [--runtime-usage RUNTIME_USAGE]
              [--runtime-buffer RUNTIME_BUFFER]
              [--num-ants-threads NUM_ANTS_THREADS]
              [--random-seed RANDOM_SEED]
              [--save-working-dir [SAVE_WORKING_DIR]] [--fail-fast FAIL_FAST]
              [--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]
              [--user_defined USER_DEFINED] [--tracking-opt-out]
              [--monitoring]
              bids_dir output_dir {participant,group,test_config,cli}

C-PAC Pipeline Runner. Copyright (C) 2022-2024 C-PAC Developers. This program
comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome
to redistribute it under certain conditions. For details, see https://fcp-
indi.github.io/docs/nightly/license or the COPYING and COPYING.LESSER files
included in the source code.

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.

options:
  -h, --help            show this help message and exit
  --pipeline-file PIPELINE_FILE, --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, --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, --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 preconfigured pipeline to run. Available
                        preconfigured pipelines: ['abcd-options', 'abcd-prep',
                        'anat-only', 'benchmark-FNIRT', 'blank', 'ccs-
                        options', 'default', 'default-deprecated', 'fmriprep-
                        ingress', 'fmriprep-options', 'fx-options', 'monkey',
                        'ndmg', 'nhp-macaque', 'preproc', 'rbc-options',
                        'rodent']. See https://fcp-
                        indi.github.io/docs/nightly/user/pipelines/preconfig
                        for more information about the preconfigured
                        pipelines.
  --aws-input-creds AWS_INPUT_CREDS, --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, --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, --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, --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, --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.
  --runtime-usage RUNTIME_USAGE, --runtime_usage RUNTIME_USAGE
                        Path to a callback.log from a prior run of the same
                        pipeline configuration (including any resource-
                        management parameters that will be applied in this
                        run, like 'n_cpus' and 'num_ants_threads'). This log
                        will be used to override per-node memory estimates
                        with observed values plus a buffer.
  --runtime-buffer RUNTIME_BUFFER, --runtime_buffer RUNTIME_BUFFER
                        Buffer to add to per-node memory estimates if
                        --runtime_usage is specified. This number is a
                        percentage of the observed memory usage.
  --num-ants-threads NUM_ANTS_THREADS, --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 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_working_dir [SAVE_WORKING_DIR]
                        Save the contents of the working directory.
  --fail-fast FAIL_FAST, --fail_fast FAIL_FAST
                        Stop worklow execution on first crash?
  --participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...], --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, --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, --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 ...], --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, --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, --skip_bids_validator
                        Skips bids validation.
  --anat-only, --anat_only
                        run only the anatomical preprocessing
  --user_defined USER_DEFINED
                        Arbitrary user defined string that will be included in
                        every output sidecar file.
  --tracking-opt-out, --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".