API Reference

This section contains detailed API documentation for all neuroLIT modules.

• Command-Line Interface
  • run_lit()
  • Overview
  • Main Functions
  • Examples
• Inference Module
  • InpaintingInferer
  • SliceWiseInpaintingInferer
  • TwoAndHalfDInpaintingInferer
  • OffsetTwoAndHalfDInpaintingInferer
  • AnomalyInferer
  • DiffusionInfererVINN
  • Overview
  • Key Concepts
• Inpainting Module
  • resolve_inference_device()
  • dilate_mask()
  • conform_nifti()
  • get_slice_from_volume()
  • inpaint_volume()
  • main()
  • Overview
  • Main Function
  • Examples
  • Integration with Other Tools
• Data Module
  • Overview
  • Submodules
  • Examples
• Networks Module
  • Overview
  • Submodules
  • Architecture Details
  • Examples
• Postprocessing Module
  • Overview
• Utils Module
  • Overview
  • Submodules
  • Examples

Quick Reference

Common Functions

from neurolit.cli import run_lit
from neurolit.inpaint_image import main as inpaint
from neurolit.data.conform import conform
from neurolit.utils.download_checkpoints import download_models

Most Used Classes

• neurolit.networks.DiffusionUnet.DiffusionUNet

• neurolit.data.datasets.BrainDataset

• neurolit.data.transforms.Compose

Entry Points

The package provides three main entry points:

1. lit-download-models: Download model checkpoints

2. lit-inpainting: Main neuroLIT command for inpainting lesions in T1-weighted brain MRI

3. lit-postprocessing: FastSurfer/FreeSurfer integration pipeline