nipoppy run

Note

This command calls the nipoppy.workflows.runner.PipelineRunner class from the Python API internally.

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

Run a pipeline.

usage: nipoppy run --dataset-root DATASET_ROOT --pipeline PIPELINE
                   [--pipeline-version PIPELINE_VERSION]
                   [--pipeline-step PIPELINE_STEP]
                   [--participant-id PARTICIPANT_ID] [--session-id SESSION_ID]
                   [--simulate] [--layout FPATH_LAYOUT]
                   [--verbosity VERBOSITY] [--dry-run] [-h]

Named Arguments

--dataset-root

Path to the root of the dataset.

--pipeline

Pipeline name, as specified in the config file.

--pipeline-version

Pipeline version, as specified in the config file.

--pipeline-step

Pipeline step, as specified in the config file (default: first step).

--participant-id

Participant ID (with or without the sub- prefix).

--session-id

Session ID (with or without the ses- prefix).

--simulate

Simulate the pipeline run without executing the generated command-line.

Global options

--layout

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

--verbosity

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

--dry-run

Print commands but do not execute them.