nipoppy reorg

Note

This command calls the nipoppy.workflows.dicom_reorg.DicomReorgWorkflow class from the Python API internally.

nipoppy reorg

(Re)organize raw (DICOM) files.

From <NIPOPPY_PROJECT_ROOT>/sourcedata/imaging/pre_reorg to <NIPOPPY_PROJECT_ROOT>/sourcedata/imaging/post_reorg

Usage

nipoppy reorg [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.

--copy-files

Copy files when reorganizing (default: create symlinks).

--check-dicoms

Read DICOM file headers when reorganizing and check if they have the “DERIVED” image type (which can be problematic for some BIDS converters). The paths to the derived DICOMs will be written to the log.

--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