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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

  • 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
  • Configuring projects

Reference

  • The global configuration file
  • String substitutions
  • 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.groups
          • nipoppy.cli.groups.OrderedAliasedGroup
          • nipoppy.cli.groups.OrderedAliasedGroupWithDotenv
        • nipoppy.cli.options
        • nipoppy.cli.pipeline_catalog
        • nipoppy.cli.NipoppyError
        • 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.JSONError
        • 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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Integrations¶

We provide tutorials to get started with using Nipoppy alongside other software tools developed by the neuroimaging community.

DataLad
DataLad logo (light) DataLad logo (dark)

Use Nipoppy with the DataLad distributed data management system for basic provenance tracking.

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DataLad
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“How to” tutorial video series
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