Command-line interface

Note

This page only describes the top-level nipoppy command. See the sidebar for more information about specific sub-commands.

nipoppy

Organize and process neuroimaging-clinical datasets.

Usage

nipoppy [OPTIONS] COMMAND [ARGS]...

Options

--version

Show the version and exit.

Run ‘nipoppy COMMAND –help’ for more information on a subcommand.

Or visit the documentation at https://nipoppy.readthedocs.io

Commands

bidsify

Run a BIDS conversion pipeline.

extract

Extract imaging-derived phenotypes (IDPs)…

init

Initialize a new dataset.

pipeline

Pipeline store operations.

process

Run a processing pipeline.

reorg

(Re)organize raw (DICOM) files.

status

Print a summary of the dataset.

track-curation

Create or update a dataset’s curation…

track-processing

Track the processing status of a pipeline.