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 <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).
- --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.
- -n, --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.
Arguments
- DATASET_ARGUMENT¶
Optional argument