Contents Menu Expand Light mode Dark mode Auto light/dark, in light mode Auto light/dark, in dark mode Skip to content
Nipoppy
Logo

Overview

  • Installation
  • Quickstart
  • User guide
    • Understanding the global configuration file
    • Populating an empty dataset
    • Organizing raw tabular data
    • Organizing raw imaging data
    • Converting a dataset to BIDS
    • Running processing pipelines
    • Tracking pipeline processing status
    • Extracting IDPs from pipeline derivatives

How-to guides

  • Initializing a new dataset
    • Starting with non-BIDS data
    • Starting with BIDS data

Reference

  • Command-line interface
    • nipoppy init
    • nipoppy status
    • nipoppy track-curation
    • nipoppy reorg
    • nipoppy bidsify
    • nipoppy run
    • nipoppy track
    • nipoppy extract
  • Python API
    • nipoppy
      • nipoppy.base
        • nipoppy.base.Base
      • nipoppy.config
        • nipoppy.config.boutiques
          • nipoppy.config.boutiques.BoutiquesConfig
        • nipoppy.config.container
          • nipoppy.config.container.ContainerConfig
          • nipoppy.config.container.ContainerInfo
        • nipoppy.config.main
          • nipoppy.config.main.Config
        • nipoppy.config.pipeline
          • nipoppy.config.pipeline.BasePipelineConfig
          • nipoppy.config.pipeline.BidsPipelineConfig
          • nipoppy.config.pipeline.ExtractionPipelineConfig
          • nipoppy.config.pipeline.PipelineInfo
          • nipoppy.config.pipeline.ProcPipelineConfig
        • nipoppy.config.pipeline_step
          • nipoppy.config.pipeline_step.AnalysisLevelType
          • nipoppy.config.pipeline_step.BasePipelineStepConfig
          • nipoppy.config.pipeline_step.BidsPipelineStepConfig
          • nipoppy.config.pipeline_step.ExtractionPipelineStepConfig
          • nipoppy.config.pipeline_step.ProcPipelineStepConfig
        • nipoppy.config.tracker
          • nipoppy.config.tracker.TrackerConfig
        • nipoppy.config.BasePipelineConfig
        • nipoppy.config.BasePipelineStepConfig
        • nipoppy.config.BidsPipelineConfig
        • nipoppy.config.BidsPipelineStepConfig
        • nipoppy.config.BoutiquesConfig
        • nipoppy.config.Config
        • nipoppy.config.ContainerConfig
        • nipoppy.config.ProcPipelineConfig
        • nipoppy.config.ProcPipelineStepConfig
        • nipoppy.config.TrackerConfig
      • nipoppy.env
        • nipoppy.env.LogColor
        • nipoppy.env.ReturnCode
      • nipoppy.layout
        • nipoppy.layout.DatasetLayout
        • nipoppy.layout.DpathInfo
        • nipoppy.layout.FpathInfo
        • nipoppy.layout.LayoutConfig
        • nipoppy.layout.OptionalFpathInfo
        • nipoppy.layout.PathInfo
      • nipoppy.logger
      • nipoppy.tabular
        • nipoppy.tabular.base
          • nipoppy.tabular.base.BaseTabular
          • nipoppy.tabular.base.BaseTabularModel
        • nipoppy.tabular.curation_status
          • nipoppy.tabular.curation_status.CurationStatusModel
          • nipoppy.tabular.curation_status.CurationStatusTable
        • nipoppy.tabular.dicom_dir_map
          • nipoppy.tabular.dicom_dir_map.DicomDirMap
          • nipoppy.tabular.dicom_dir_map.DicomDirMapModel
        • nipoppy.tabular.manifest
          • nipoppy.tabular.manifest.Manifest
          • nipoppy.tabular.manifest.ManifestModel
        • nipoppy.tabular.processing_status
          • nipoppy.tabular.processing_status.ProcessingStatusModel
          • nipoppy.tabular.processing_status.ProcessingStatusTable
        • nipoppy.tabular.CurationStatusTable
        • nipoppy.tabular.Manifest
        • nipoppy.tabular.ProcessingStatusTable
      • nipoppy.utils
      • nipoppy.workflows
        • nipoppy.workflows.base
          • nipoppy.workflows.base.BaseWorkflow
        • nipoppy.workflows.bids_conversion
          • nipoppy.workflows.bids_conversion.BidsConversionRunner
        • nipoppy.workflows.dataset_init
          • nipoppy.workflows.dataset_init.InitWorkflow
        • nipoppy.workflows.dataset_status
          • nipoppy.workflows.dataset_status.StatusWorkflow
        • nipoppy.workflows.dicom_reorg
          • nipoppy.workflows.dicom_reorg.DicomReorgWorkflow
        • nipoppy.workflows.extractor
          • nipoppy.workflows.extractor.ExtractionRunner
        • nipoppy.workflows.pipeline
          • nipoppy.workflows.pipeline.BasePipelineWorkflow
        • nipoppy.workflows.runner
          • nipoppy.workflows.runner.PipelineRunner
        • nipoppy.workflows.track_curation
          • nipoppy.workflows.track_curation.TrackCurationWorkflow
        • nipoppy.workflows.tracker
          • nipoppy.workflows.tracker.PipelineTracker
        • nipoppy.workflows.BasePipelineWorkflow
        • nipoppy.workflows.BaseWorkflow
        • nipoppy.workflows.BidsConversionRunner
        • nipoppy.workflows.DicomReorgWorkflow
        • nipoppy.workflows.ExtractionRunner
        • nipoppy.workflows.InitWorkflow
        • nipoppy.workflows.PipelineRunner
        • nipoppy.workflows.PipelineTracker
        • nipoppy.workflows.StatusWorkflow
        • nipoppy.workflows.TrackCurationWorkflow
  • File schemas

Other

  • What’s new
  • Contributing
  • Glossary
Back to top
View this page
Edit this page

nipoppy.config.pipeline_step¶

Pipeline step configuration.

Classes¶

AnalysisLevelType

Pipeline step types.

BasePipelineStepConfig

Schema for processing pipeline step configuration.

BidsPipelineStepConfig

Schema for BIDS pipeline step configuration.

ExtractionPipelineStepConfig

Schema for extraction pipeline step configuration.

ProcPipelineStepConfig

Schema for processing pipeline step configuration.
Next
nipoppy.config.pipeline_step.AnalysisLevelType
Previous
nipoppy.config.pipeline.ProcPipelineConfig
Copyright © 2024, NeuroDataScience-ORIGAMI Lab
Made with Sphinx and @pradyunsg's Furo
On this page
  • nipoppy.config.pipeline_step
    • Classes