Lesion inpainting (LIT) integration

[ClePol]

Summary

This PR adds optional neuroLIT integration to FastSurfer for lesion-aware runs via --lesion_mask.

What changes

• call lit-inpainting before VINN segmentation when --lesion_mask is provided
• call lit-postprocessing after segmentation / recon-surf to restore lesion-aware outputs and reports
• forward --keepgeom to neuroLIT in native-image mode
• mirror FastSurfer --no_biasfield behavior by skipping only the segstats that are unsupported by the available inputs instead of crashing
• add/update documentation for LIT usage, examples, outputs, and module overview
• preload LIT checkpoints in the FastSurfer Docker image and set a deterministic XDG_DATA_HOME for neurolit

Testing

• clean neurolit wheel install and standalone CUDA inpainting passed
• standalone LIT Docker test passed
• full FastSurfer + LIT integration passed
• full FastSurfer + LIT integration with --no_biasfield passed
• anisotropic 1.0x1.0x1.2 --keepgeom --seg_only integration passed and preserved image size / voxel size through the inpainted and downstream FastSurfer outputs
• negative --surf_only --lesion_mask case fails early with a clear error if prior inpainting outputs are missing

[Copilot]

Pull request overview

Integrates the optional neuroLIT Lesion Inpainting Tool (LIT) into the FastSurfer pipeline so that lesion-aware processing can be triggered via --lesion_mask, including Docker preloading of LIT checkpoints and updated documentation.

Changes:

• Add --lesion_mask support in run_fastsurfer.sh to run lit-inpainting before segmentation and lit-postprocessing after segmentation/surfaces, with special handling for --no_biasfield.
• Add neurolit as a Python dependency and preload LIT models in the Docker image with deterministic XDG_DATA_HOME.
• Add documentation pages/updates describing LIT usage, examples, outputs, and module overview entries.

Reviewed changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
tools/Docker/Dockerfile	Pins XDG_DATA_HOME and pre-downloads LIT models during image build.
run_fastsurfer.sh	Adds --lesion_mask flag and runs LIT inpainting/postprocessing around the existing pipeline.
pyproject.toml	Adds neurolit dependency for LIT CLIs.
doc/scripts/lit.rst	New script documentation page explaining LIT integration and outputs.
doc/scripts/index.rst	Adds lit.rst to scripts documentation index.
doc/scripts/RUN_FASTSURFER.md	Documents the new --lesion_mask CLI option.
doc/overview/modules/index.rst	Adds LIT to module overview index.
doc/overview/modules/LIT.md	New module overview page describing LIT and its outputs.
doc/overview/intro.rst	Mentions LIT as a FastSurfer capability in the intro overview.
doc/overview/OUTPUT_FILES.md	Documents LIT-related outputs and file locations.
doc/overview/EXAMPLES.md	Adds a new end-to-end example for running FastSurfer with --lesion_mask.
README.md	Mentions neurolit/LIT in modules list and adds the LIT citation.
FastSurferCNN/data_loader/conform.py	Hardens dtype-name handling in is_conform() logging/check labeling.

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