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Nipoppy
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Overview

  • Why Nipoppy?
    • The principles
    • The use cases
  • Installation
  • Quickstart

Tutorials

  • Convert MRI sourcedata to BIDS
  • Run MRIQC on a BIDS dataset
  • Video series
  • Integrations
    • DataLad

Explanations

  • Study specification
  • The recruitment file
  • The manifest file
  • IDP specification

How-to guides

  • User guide (legacy)
    • Understanding the global configuration file
    • Populating an empty dataset
    • Organizing raw imaging data
    • Converting a dataset to BIDS
    • Running processing pipelines
    • Tracking pipeline processing status
    • Extracting IDPs from pipeline derivatives
  • Initializing a new dataset
    • Starting with non-BIDS data
    • Starting with BIDS data
  • Creating the manifest file
    • Example script 1
    • Example script 2
    • Example script 3
  • Reorganizing imaging sourcedata
  • Organizing tabular data
  • Using Nipoppy with Docker
  • Installing a pipeline
  • Running a pipeline
  • Tracking pipeline statuses
  • Parallelizing pipeline runs
    • HPC job scheduling
    • Local parallelization
  • Developing a Nipoppy pipeline

Reference

  • Command-line interface
    • nipoppy init
    • nipoppy status
    • nipoppy track-curation
    • nipoppy reorg
    • nipoppy bidsify
    • nipoppy process
    • nipoppy track-processing
    • nipoppy extract
    • nipoppy pipeline
    • nipoppy pipeline search
    • nipoppy pipeline create
    • nipoppy pipeline install
    • nipoppy pipeline list
    • nipoppy pipeline validate
    • nipoppy pipeline upload
  • Python API
    • nipoppy
      • nipoppy.base
        • nipoppy.base.Base
      • nipoppy.cli
        • nipoppy.cli.options
        • nipoppy.cli.pipeline_catalog
        • nipoppy.cli.NipoppyError
        • nipoppy.cli.OrderedAliasedGroup
        • nipoppy.cli.ReturnCode
      • nipoppy.config
        • nipoppy.config.boutiques
          • nipoppy.config.boutiques.BoutiquesConfig
        • nipoppy.config.container
          • nipoppy.config.container.ContainerConfig
          • nipoppy.config.container.ContainerInfo
        • nipoppy.config.hpc
          • nipoppy.config.hpc.HpcConfig
        • nipoppy.config.main
          • nipoppy.config.main.Config
          • nipoppy.config.main.PipelineVariables
        • nipoppy.config.pipeline
          • nipoppy.config.pipeline.BIDSificationPipelineConfig
          • nipoppy.config.pipeline.BasePipelineConfig
          • nipoppy.config.pipeline.ExtractionPipelineConfig
          • nipoppy.config.pipeline.PipelineInfo
          • nipoppy.config.pipeline.ProcessingPipelineConfig
        • 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.console
      • nipoppy.container
        • nipoppy.container.ApptainerHandler
        • nipoppy.container.BareMetalHandler
        • nipoppy.container.ContainerHandler
        • nipoppy.container.DockerHandler
        • nipoppy.container.SingularityHandler
      • nipoppy.env
        • nipoppy.env.ContainerCommandEnum
        • nipoppy.env.PipelineTypeEnum
      • nipoppy.exceptions
        • nipoppy.exceptions.ConfigError
        • nipoppy.exceptions.ContainerError
        • nipoppy.exceptions.ExecutionError
        • nipoppy.exceptions.FileOperationError
        • nipoppy.exceptions.LayoutError
        • nipoppy.exceptions.NipoppyError
        • nipoppy.exceptions.TabularError
        • nipoppy.exceptions.TerminatedByUserError
        • nipoppy.exceptions.WorkflowError
        • nipoppy.exceptions.ReturnCode
      • nipoppy.layout
        • nipoppy.layout.DatasetLayout
        • nipoppy.layout.DpathInfo
        • nipoppy.layout.FpathInfo
        • nipoppy.layout.LayoutConfig
        • nipoppy.layout.OptionalDpathInfo
        • nipoppy.layout.OptionalFpathInfo
        • nipoppy.layout.PathInfo
      • nipoppy.logger
        • nipoppy.logger.LogColor
        • nipoppy.logger.NipoppyLogger
      • nipoppy.pipeline_validation
        • nipoppy.pipeline_validation.PipelineValidationError
      • nipoppy.study
        • nipoppy.study.Study
      • 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.utils
        • nipoppy.utils.bids
        • nipoppy.utils.fileops
        • nipoppy.utils.html
          • nipoppy.utils.html.SelectiveHTMLStripper
        • nipoppy.utils.utils
      • nipoppy.workflows
        • nipoppy.workflows.base
          • nipoppy.workflows.base.BaseDatasetWorkflow
          • nipoppy.workflows.base.BaseWorkflow
          • nipoppy.workflows.base.CommandRunner
          • nipoppy.workflows.base.LogPrefix
        • nipoppy.workflows.bids_conversion
          • nipoppy.workflows.bids_conversion.BIDSificationRunner
        • 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.pipeline_store
          • nipoppy.workflows.pipeline_store.create
            • nipoppy.workflows.pipeline_store.create.PipelineCreateWorkflow
          • nipoppy.workflows.pipeline_store.install
            • nipoppy.workflows.pipeline_store.install.PipelineInstallWorkflow
          • nipoppy.workflows.pipeline_store.list
            • nipoppy.workflows.pipeline_store.list.PipelineListWorkflow
          • nipoppy.workflows.pipeline_store.search
            • nipoppy.workflows.pipeline_store.search.PipelineSearchWorkflow
          • nipoppy.workflows.pipeline_store.upload
            • nipoppy.workflows.pipeline_store.upload.PipelineUploadWorkflow
          • nipoppy.workflows.pipeline_store.validate
            • nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow
        • nipoppy.workflows.processing_runner
          • nipoppy.workflows.processing_runner.ProcessingRunner
        • nipoppy.workflows.runner
          • nipoppy.workflows.runner.Runner
        • nipoppy.workflows.services
          • nipoppy.workflows.services.boutiques
            • nipoppy.workflows.services.boutiques.BoshRunnerCallable
            • nipoppy.workflows.services.boutiques.CommandBuilder
            • nipoppy.workflows.services.boutiques.ErrorBuilder
          • nipoppy.workflows.services.hpc
            • nipoppy.workflows.services.hpc.HPCRunner
        • nipoppy.workflows.track_curation
          • nipoppy.workflows.track_curation.TrackCurationWorkflow
        • nipoppy.workflows.tracker
          • nipoppy.workflows.tracker.PipelineTracker
      • nipoppy.zenodo_api
        • nipoppy.zenodo_api.ChecksumError
        • nipoppy.zenodo_api.ZenodoAPIError
        • nipoppy.zenodo_api.ZenodoAPI
      • nipoppy.NipoppyDataRetriever
  • File schemas

Other

  • What’s new
  • Team
  • 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.

ExtractionPipelineStepConfig

Schema for extraction pipeline step configuration.

ProcPipelineStepConfig

Schema for processing pipeline step configuration.
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nipoppy.config.pipeline_step.AnalysisLevelType
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