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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
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
Python API
- nipoppy
File schemas

Other

What’s new
Team
Contributing
Glossary

nipoppy.workflows.base.CommandRunner¶

class nipoppy.workflows.base.CommandRunner¶: Protocol for functions that run commands, used for strategy injection.

nipoppy.workflows.base.LogPrefix

nipoppy.workflows.base.BaseWorkflow

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nipoppy.workflows.base.CommandRunner
- nipoppy.workflows.base.CommandRunner