nipoppy bidsify

Note

This command calls the nipoppy.workflows.bids_conversion.BidsConversionRunner class from the Python API internally.

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

Run a BIDS conversion pipeline.

usage: nipoppy bidsify --pipeline PIPELINE_NAME
                       [--pipeline-version PIPELINE_VERSION]
                       [--pipeline-step PIPELINE_STEP]
                       [--participant-id PARTICIPANT_ID]
                       [--session-id SESSION_ID] [--simulate]
                       [--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

--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

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.