dipy_auto#

Synopsis#

Run diffusion pipelines based on configuration files.

Usage#

dipy_auto [OPTIONS] input_files

Input Parameters#

  • input_files

    Input files passed to the pipeline. File types are detected automatically from their extensions (case-insensitive):

    • .toml — pipeline configuration file.

    • .nii / .nii.gz — DWI NIfTI file.

    • .bval / .bvals — b-values file.

    • .bvec / .bvecs — b-vectors file.

    • *report*.html — HTML report; all other inputs are ignored and the report is served via a local HTTP server.

    With --bids, the arguments follow the BIDS-App convention instead: dipy_auto <bids_dir> [<output_dir>] [participant].

General Options#

  • --t1_file

    Path to the T1 file. Resolved from the dataset with --bids. (default: None)

  • --mask_file

    Path to the brain mask file. (default: None)

  • --dwi_opp_phase_file

    Path to the opposite phase DWI file (for phase correction). Resolved from the fieldmaps of the dataset with --bids. (default: None)

  • --bids

    Treat the inputs as a BIDS dataset and run the pipeline on every diffusion acquisition it contains, writing BIDS derivatives. (default: False)

  • --bids_folder

    Path to the BIDS dataset root, as an alternative to passing it positionally. Requires --bids. (default: None)

  • --participant_label

    Subject labels to process, with or without the sub- prefix. All subjects are processed when omitted. (default: None)

  • --session_label

    Session labels to process, with or without the ses- prefix. (default: None)

  • --acquisition_label

    acq- labels to process. (default: None)

  • --run_label

    run- labels to process. (default: None)

  • --stop_on_error

    Stop a BIDS batch at the first acquisition that fails instead of reporting it and carrying on. (default: False)

  • --atlas_tractogram

    Path to atlas tractogram for registration (dipy_slr). If not provided and dipy_slr is in the pipeline, will auto-download HCP 30-bundle atlas. (default: None)

  • --bundle_atlas_dir

    Path to bundle atlas directory for segmentation (dipy_recobundles). If not provided and dipy_recobundles is in the pipeline, will auto-download HCP 30-bundle atlas. (default: None)

  • --interactive_mode

    Enable interactive mode for pipeline customization. (default: False)

  • --pipeline_type

    Predefined pipeline type: ‘preprocessing’, ‘dti_only’, ‘tractography’ or ‘full’. Use –list-pipelines to see all available pipelines. (default: None)

  • --start

    Stage name to start execution from. Earlier stages will be skipped, but their outputs must exist on disk. Use this to resume a failed pipeline or re-run later stages with different parameters. (default: None)

  • --dry_run

    Show execution plan without running commands. (default: False)

  • --list_pipelines

    List all available predefined pipelines and exit. (default: False)

Output Options#

  • --out_dir

    Output directory. When omitted, the out_dir of the [io] section of the configuration, or the current directory. With --bids, the root of the derivative dataset, defaulting to <bids_dir>/derivatives/dipy. (default: current directory)

  • --out_report

    Path to the report file. (default: reports.toml)

References#

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.

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