nipoppy doughnut

Note

This command calls the nipoppy.workflows.doughnut.DoughnutWorkflow class from the Python API internally.

Logfiles for this command can be found in <DATASET_ROOT>/scratch/logs/doughnut.

Create/update a dataset’s doughnut file.

usage: nipoppy doughnut --dataset-root DATASET_ROOT [--empty] [--regenerate]
                        [--layout FPATH_LAYOUT] [--verbosity {0,1,2,3}]
                        [--dry-run] [-h]

Named Arguments

--dataset-root

Path to the root of the dataset.

--empty

Set all statuses to False in newly added records (regardless of what is on disk). May be useful to reduce runtime.

--regenerate

Regenerate the doughnut file even if it already exists (default: only append rows for new records)

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.