nipoppy init

Note

This command calls the nipoppy.workflows.dataset_init.InitWorkflow class from the Python API internally.

nipoppy init

Initialize a new dataset.

Usage

nipoppy init [OPTIONS]

Options

--dataset <dpath_root>

Path to the root of the dataset. Default: current working directory or the closest parent directory that contains a .nipoppy directory.

--bids-source <bids_source>

Path to a BIDS dataset to initialize the layout with.

-f, --force

Create a nipoppy dataset even if there are already files present (may clobber existing files).

--mode <mode>

If using a BIDS source, specify whether to copy, move, or symlink the files.

Options:

copy | move | symlink

--dry-run

Print commands but do not execute them.

-v, --verbose

Verbose mode (Show DEBUG messages).

--layout <fpath_layout>

Path to a custom layout specification file, to be used instead of the default layout.

Environment variables

NIPOPPY_LAYOUT

Provide a default for --layout