CLI reference

The preferred public command is:

hemispec

The subcommands below were checked against the current toolkit interface on 2026-09-05. Re-check them before public release if the toolkit source or package name changes.

Current subcommands

hemispec quickstart      run the public-safe synthetic smoke test
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

Current main can pre-download the DGN checkpoints tracked by Git LFS:

hemispec models --install

If this is skipped, workflow, infer, run, and the GUI download the DGN checkpoints from the repository's main Git LFS media on first model use.

The CLI still supports --with-classifier, but it is not a working installation recommendation at present because required feature_names.csv media URLs return HTTP 404. Obtain classifier assets from a local Git LFS checkout and use --classifier-model-dir or HEMISPEC_CLASSIFIER_MODEL_DIR; see the known limitation.

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.

The released classifier accepts only features from its compatible Glasser 1.5 mm atlas: homologous labels 1..180 on the left and 1001..1180 on the right. A custom atlas may be used for ROI export, but not with the released classifier.

Reporting

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

ANS/RNS and the cross-hemispheric DGN framework originate from Wang et al. (2024); see Citation.