Command-Line Interface

neurolit.cli.run_lit()[source]

Run the neuroLIT CLI.

This function serves as the main entry point for the Lesion Inpainting Tool command-line interface. It parses command-line arguments, validates inputs, and initiates the inpainting process.

Overview

The CLI module provides command-line interfaces for running neuroLIT operations.

Main Functions

lit-inpainting

neurolit.cli.run_lit()

Entry point for the main lit-inpainting command. This is the primary interface for running the full neuroLIT pipeline.

Usage:

lit-inpainting --input_image T1w.nii.gz \\
       --mask_image lesion_mask.nii.gz \\
       --output_directory output

Parameters:

--input_image: Path to input T1-weighted image
--mask_image: Path to lesion mask
--output_directory: Output directory path
--dilate: Number of dilation iterations (default: 0)
--fastsurfer_dir: Treat the output directory as a FastSurfer subject directory
--device: Device to use (cuda/cpu)

Examples

Basic Usage

from neurolit.cli import run_lit
import sys

# Simulate command-line arguments
sys.argv = [
    'run_lit',
    '--input_image', 'T1w.nii.gz',
    '--mask_image', 'mask.nii.gz',
    '--output_directory', 'output'
]

run_lit()

Programmatic Usage

import subprocess

cmd = [
    'run_lit',
    '--input_image', 'T1w.nii.gz',
    '--mask_image', 'mask.nii.gz',
    '--output_directory', 'output',
    '--dilate', '2'
]

result = subprocess.run(cmd, capture_output=True, text=True)
print(result.stdout)