Usage

The follow section of the book contains information about hte various NiftyOne workflows, executing NiftyOne both on local machines and via containers. Additionally, there includes a sub-section on advanced NiftyOne usage.

Command line interface (CLI)

The following can also be seen by running niftyone -h in your terminal.

Below are all arguments of the NiftyOne CLI, separated by analysis level. In most cases, only the required arguments are needed.

usage: niftyone bids_dir output_dir analysis_level [options]

NiftyOne is a comphrensive tool designed to aid large-scale QC of BIDS datasets through
visualization and quantitative metrics.

positional arguments:
  bids_dir              Path to BIDS dataset
  output_dir            Path to output directory
  analysis_level        Analysis level

options:
  -h, --help            show this help message and exit
  --overwrite, -x       Overwrite previous results
  --verbose, -v         Verbose logging.

participant level options:
  --participant-label LABEL, --sub LABEL
                        Participant to analyze (default: all)
  --index PATH          Pre-computed bids2table index path (default: {bids_dir}/index.b2t)
  --qc-dir PATH         Path to pre-computed QC outputs
                        (default: {bids_dir}/derivatives/mriqc)
  --workers COUNT, -w COUNT
                        Number of worker processes. Setting to -1 runs as many processes as
                        there are cores available. (default: 1)

group level options:
  --ds-name DATASET     Name of NiftyOne dataset.

launch level options:
  --qc-key LABEL        Extra identifier for the QC session

For more information about the different analysis levels, see the workflows page.