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 <DATASET_ROOT>/logs/dicom_reorg.

(Re)organize raw (DICOM) files, from the (<DATASET_ROOT>/sourcedata/imaging/pre_reorg) to (<DATASET_ROOT>/sourcedata/imaging/post_reorg).

usage: nipoppy reorg [--copy-files] [--check-dicoms] [--layout FPATH_LAYOUT]
                     [--verbosity {0,1,2,3}] [--dry-run] [-h]
                     dataset_root

Positional Arguments

dataset_root

Path to the root of the dataset.

Named Arguments

--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.

Global options

--layout

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

--verbosity

Possible choices: 0, 1, 2, 3

Verbosity level, from 0 (least verbose) to 3 (most verbose). Default: 2.

--dry-run

Print commands but do not execute them.