CLI reference

The preferred public command is:

hemispec

The subcommands below were checked against the current toolkit interface on 2026-06-29. Re-check them before public release if the toolkit source or package name changes.

Current subcommands

hemispec models          list or pre-download released trained DGN model bundles
hemispec infer           run trained DGN inference on preprocessed GM maps
hemispec compute         compute ANS/RNS maps from actual and reconstructed GM maps
hemispec run             run DGN inference followed by ANS/RNS computation
hemispec workflow        run bilateral DGN and generate ANS/RNS outputs
hemispec trt             test-retest reliability validation
hemispec specificity     structural specificity validation
hemispec hemi-classify   ROI-level hemisphere-classifier validation

Command naming

Use hemispec for the command-line interface and hemispec-gui for the graphical interface.

Model asset prefetch

Wheel/PyPI installs can pre-download the released DGN checkpoints and classifier bundle:

hemispec models --install --with-classifier

If this is skipped, workflow, infer, run, and the GUI download the released DGN checkpoints automatically on first model use.

ROI outputs

ROI export is currently exposed through options on compute, run, and workflow. For workflow, ROI export is optional and can be skipped with --no-roi-table; classifier validation is opt-in with --run-classifier and requires ROI features.

--roi-atlas
--roi-out-csv
--roi-label-table
--roi-stat
--no-roi-table
--run-classifier

There is not yet a standalone roi subcommand.

Reporting

There is not yet a standalone report subcommand. Reporting should be treated as a planned feature until implemented.