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Overview

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

Tutorials

Run MRIQC on a BIDS dataset
Integrations
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- DataLad
Video series
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- What is?
- How to?

Explanations

The manifest file

How-to guides

User guide (legacy)
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Initializing a new dataset
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- Starting with non-BIDS data
- Starting with BIDS data
Creating the manifest file
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Organizing tabular data
Installing a pipeline
Running a pipeline
Tracking pipeline statuses
Parallelizing pipeline runs
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- HPC job scheduling
- Local parallelization
Developing a Nipoppy pipeline

Reference

Command-line interface
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Python API
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- nipoppy
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  - nipoppy.base
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    - nipoppy.base.Base
  - nipoppy.cli
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  - nipoppy.config
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    - nipoppy.config.boutiques
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      - nipoppy.config.boutiques.BoutiquesConfig
    - nipoppy.config.container
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      - nipoppy.config.container.ContainerConfig
      - nipoppy.config.container.ContainerInfo
    - nipoppy.config.hpc
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      - nipoppy.config.hpc.HpcConfig
    - nipoppy.config.main
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      - nipoppy.config.main.Config
      - nipoppy.config.main.PipelineVariables
    - nipoppy.config.pipeline
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    - nipoppy.config.pipeline_step
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    - nipoppy.config.tracker
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  - nipoppy.console
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  - nipoppy.layout
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  - nipoppy.logger
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  - nipoppy.tabular
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    - nipoppy.tabular.base
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      - nipoppy.tabular.base.BaseTabular
      - nipoppy.tabular.base.BaseTabularModel
    - nipoppy.tabular.curation_status
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      - nipoppy.tabular.curation_status.CurationStatusModel
      - nipoppy.tabular.curation_status.CurationStatusTable
    - nipoppy.tabular.dicom_dir_map
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      - nipoppy.tabular.dicom_dir_map.DicomDirMap
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    - nipoppy.tabular.manifest
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      - nipoppy.tabular.manifest.Manifest
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    - nipoppy.tabular.processing_status
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      - nipoppy.tabular.processing_status.ProcessingStatusModel
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  - nipoppy.utils
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    - nipoppy.utils.bids
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  - nipoppy.workflows
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    - nipoppy.workflows.base
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    - nipoppy.workflows.bids_conversion
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      - nipoppy.workflows.bids_conversion.BIDSificationRunner
    - nipoppy.workflows.dataset_init
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      - nipoppy.workflows.dataset_init.InitWorkflow
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File schemas

Other

What’s new
Contributing
Glossary

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nipoppy.workflows.processing_runner¶

PipelineRunner workflow.

Classes¶

ProcessingRunner

Pipeline runner.

nipoppy.workflows.processing_runner.ProcessingRunner

nipoppy.workflows.pipeline_store.validate.PipelineValidateWorkflow

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