nipoppy reorg

Note

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

Logfiles for this command can be found in {{dpath_logs}}/dicom_reorg.

nipoppy reorg

(Re)organize raw (DICOM) files.

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

nipoppy reorg [OPTIONS] [DATASET_ARGUMENT]

Options

--dataset <dpath_root>

Path to the root of the dataset (default is current working directory).

Default:

PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/nipoppy/checkouts/608/docs/source')

--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.

--layout <fpath_layout>

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

-n, --dry-run

Print commands but do not execute them.

-v, --verbose

Verbose mode (Show DEBUG messages).

Arguments

DATASET_ARGUMENT

Optional argument