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Nipoppy
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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

Reference

  • Command-line interface
    • nipoppy init
    • nipoppy doughnut
    • nipoppy reorg
    • nipoppy convert
    • nipoppy run
    • nipoppy track
  • 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.ProcPipelineConfig
        • nipoppy.config.pipeline_step
          • nipoppy.config.pipeline_step.AnalysisLevelType
          • nipoppy.config.pipeline_step.BasePipelineStepConfig
          • nipoppy.config.pipeline_step.BidsPipelineStepConfig
          • 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.bagel
          • nipoppy.tabular.bagel.Bagel
          • nipoppy.tabular.bagel.BagelModel
        • nipoppy.tabular.base
          • nipoppy.tabular.base.BaseTabular
          • nipoppy.tabular.base.BaseTabularModel
        • nipoppy.tabular.dicom_dir_map
          • nipoppy.tabular.dicom_dir_map.DicomDirMap
          • nipoppy.tabular.dicom_dir_map.DicomDirMapModel
        • nipoppy.tabular.doughnut
          • nipoppy.tabular.doughnut.Doughnut
          • nipoppy.tabular.doughnut.DoughnutModel
        • nipoppy.tabular.manifest
          • nipoppy.tabular.manifest.Manifest
          • nipoppy.tabular.manifest.ManifestModel
        • nipoppy.tabular.Bagel
        • nipoppy.tabular.Doughnut
        • nipoppy.tabular.Manifest
      • 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.dicom_reorg
          • nipoppy.workflows.dicom_reorg.DicomReorgWorkflow
        • nipoppy.workflows.doughnut
          • nipoppy.workflows.doughnut.DoughnutWorkflow
        • nipoppy.workflows.pipeline
          • nipoppy.workflows.pipeline.BasePipelineWorkflow
        • nipoppy.workflows.runner
          • nipoppy.workflows.runner.PipelineRunner
        • nipoppy.workflows.tracker
          • nipoppy.workflows.tracker.PipelineTracker
        • nipoppy.workflows.BasePipelineWorkflow
        • nipoppy.workflows.BaseWorkflow
        • nipoppy.workflows.BidsConversionRunner
        • nipoppy.workflows.DicomReorgWorkflow
        • nipoppy.workflows.DoughnutWorkflow
        • nipoppy.workflows.InitWorkflow
        • nipoppy.workflows.PipelineRunner
        • nipoppy.workflows.PipelineTracker
  • File schemas

Other

  • What’s new
  • Contributing
  • Glossary
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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.

ProcPipelineStepConfig

Schema for processing pipeline step configuration.
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nipoppy.config.pipeline_step.AnalysisLevelType
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nipoppy.config.pipeline.ProcPipelineConfig
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    • Classes