Postprocessing Module

The postprocessing module provides tools for integrating lesion masks into FastSurfer/FreeSurfer outputs.

Overview

The recommended way to run postprocessing is via the lit-postprocessing command-line tool.

Command-Line Usage

lit-postprocessing \
    --subject-id SUBJECT_ID \
    --subjects-dir /path/to/subjects_dir

This tool performs the following steps: 1. Maps the lesion mask into all relevant FastSurfer segmentation volumes (e.g., aparc+aseg.mgz). 2. Generates anatomy reports (replaced, reduced, and adjacent labels). 3. Runs volumetric statistics (segstats) for the lesion-masked volumes. 4. Projects the lesion mask onto cortical surfaces and performs surface masking.

For more details on configuration, see segstats_config.json and surfstats_config.json in the neurolit/postprocessing directory.