.. neuroLIT - Neuro Lesion Inpainting Tool documentation master file

Welcome to the neuroLIT Documentation!
======================================

**neuroLIT (Neuro Lesion Inpainting Tool)** is a tool for inpainting lesions in brain MRI images, independent of their shape or appearance, for further downstream analysis.

neuroLIT with FastSurfer can be run by directly running `FastSurfer <https://deep-mi.org/fastsurfer/>`_. For other tools and FreeSurfer use the neuroLIT repository.

.. image:: overview.png
   :alt: neuroLIT Overview
   :align: left
   :width: 100%

🔥 **Key Features**
-------------------

* Inpaints lesions of any shape or appearance in T1-weighted MRI images
* Standalone operation or integration with FastSurfer
* Docker and Singularity containerization support
* PyPI package available for easy installation
* Surface and segmentation masking capabilities

Quick Start
-----------

Using Docker/Singularity (Recommended)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   git clone https://github.com/Deep-MI/neurolit.git && cd neurolit
   ./neurolit/scripts/run_lit_containerized.sh --input_image T1w.nii.gz \\
       --mask_image lesion_mask.nii.gz --output_directory output_directory

Using PyPI Package
~~~~~~~~~~~~~~~~~~

.. code-block:: bash

   # Install the package
   pip install neurolit
   
   # Download model checkpoints
   lit-download-models
   
   # Run LIT
   lit-inpainting --input_image T1w.nii.gz --lesion_mask lesion_mask.nii.gz \\
       --output_directory output_directory --dilate 2

.. toctree::
   :maxdepth: 2
   :caption: User Guide

   installation
   usage
   downstream_analysis
   training

.. toctree::
   :maxdepth: 2
   :caption: Development

   contributing
   api/modules
   documentation

.. toctree::
   :maxdepth: 1
   :caption: Reference

   citation

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`