CLI Reference¶

The voxelkit command gives you everything in the library without writing a line of Python.

voxelkit --help

There are nine commands total:

Command	What it does
`inspect`	Print file metadata as JSON
`preview`	Save a PNG slice to disk
`report`	Print a QA report as JSON
`report-batch`	QA report for every file in a directory (`--html` for a self-contained HTML report)
`anonymise`	Scrub PHI from every `.dcm` under a directory
`convert`	Convert a DICOM file or series to a NIfTI volume
`embed-report`	Per-dimension + per-sample embedding QA
`embed-preview`	Render an embedding matrix as a heatmap PNG
`gui`	Launch the local Streamlit interface

Quick orientation¶

Every command that outputs data prints JSON to stdout. You can pipe it, save it, or format it however you like:

# pipe to jq for pretty inspection
voxelkit inspect myfile.nii.gz | jq '.shape'

# save to a file
voxelkit report myfile.h5 > report.json

Commands that generate images always require --output:

voxelkit preview myfile.nii.gz --plane axial --output preview.png

voxelkit --help            # top-level help
voxelkit inspect --help    # help for a specific command

Use the sidebar to jump to any individual command.