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Nipoppy
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Overview

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

Tutorials

  • Run MRIQC on a BIDS dataset

Explanations

  • The manifest file

How-to guides

  • User guide (legacy)
    • 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
  • 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
  • Adding a pipeline to a dataset
  • Running a 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 search
    • nipoppy pipeline install
    • nipoppy pipeline list
    • nipoppy pipeline validate
    • nipoppy pipeline upload
  • 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.hpc
          • nipoppy.config.hpc.HpcConfig
        • nipoppy.config.main
          • nipoppy.config.main.Config
          • nipoppy.config.main.PipelineVariables
        • 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.console
      • nipoppy.env
        • nipoppy.env.LogColor
        • nipoppy.env.PipelineTypeEnum
        • nipoppy.env.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.pipeline_validation
      • 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.BaseDatasetWorkflow
          • 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.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.validate
            • nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow
          • nipoppy.workflows.pipeline_store.zenodo
            • nipoppy.workflows.pipeline_store.zenodo.ZenodoUploadWorkflow
        • 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.BaseDatasetWorkflow
        • nipoppy.workflows.BasePipelineWorkflow
        • nipoppy.workflows.BaseWorkflow
        • nipoppy.workflows.BidsConversionRunner
        • nipoppy.workflows.DicomReorgWorkflow
        • nipoppy.workflows.ExtractionRunner
        • nipoppy.workflows.InitWorkflow
        • nipoppy.workflows.PipelineInstallWorkflow
        • nipoppy.workflows.PipelineListWorkflow
        • nipoppy.workflows.PipelineRunner
        • nipoppy.workflows.PipelineTracker
        • nipoppy.workflows.PipelineValidateWorkflow
        • nipoppy.workflows.StatusWorkflow
        • nipoppy.workflows.TrackCurationWorkflow
      • nipoppy.zenodo_api
        • nipoppy.zenodo_api.InvalidChecksumError
        • nipoppy.zenodo_api.ZenodoAPIError
        • nipoppy.zenodo_api.ZenodoAPI
  • File schemas

Other

  • What’s new
  • Contributing
  • Glossary
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Attention

This is the legacy user guide and may contain information that is out-of-date.

User guide (legacy)¶

This guide covers the main steps in the Nipoppy protocol:

  • 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
Next
Understanding the global configuration file
Previous
The manifest file
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