Skip to content

README.md

Latest commit

 

History

History
137 lines (102 loc) · 3.79 KB

README.md

File metadata and controls

137 lines (102 loc) · 3.79 KB

Convenience Scripts

This directory contains convenience wrapper scripts for running the Alzheimer MRI Processing Pipeline stages. These scripts simplify execution for non-technical users by wrapping the Python CLI commands.

Directory Structure

  • unix_based_system/ - Shell scripts (.sh) for Linux and macOS
  • windows_based_system/ - Batch scripts (.bat) for Windows

Available Scripts

Individual Stage Scripts

Run these scripts if you want to execute stages one-by-one and monitor progress:

Unix/Linux/macOS:

./scripts/unix_based_system/run_environment_setup.sh
./scripts/unix_based_system/run_data_preparation.sh
./scripts/unix_based_system/run_nifti_processing.sh
./scripts/unix_based_system/run_image_processing.sh

Windows:

scripts\windows_based_system\run_environment_setup.bat
scripts\windows_based_system\run_data_preparation.bat
scripts\windows_based_system\run_nifti_processing.bat
scripts\windows_based_system\run_image_processing.bat

Full Pipeline Scripts

Run these scripts if you want to execute the entire pipeline end-to-end in one go. Only use these if you have sufficient machine resources and can leave the process running for several hours.

Unix/Linux/macOS:

./scripts/unix_based_system/run_full_pipeline.sh

Windows:

scripts\windows_based_system\run_full_pipeline.bat

What Each Script Does

run_environment_setup.sh / run_environment_setup.bat

  • Runs environment setup with GPU detection
  • Auto-installs PyTorch with appropriate CUDA version
  • Performs full performance test

run_data_preparation.sh / run_data_preparation.bat

  • Runs data splitting (train/val/test)
  • Runs data analysis
  • Generates manifest files

run_nifti_processing.sh / run_nifti_processing.bat

Runs all NIfTI processing substages sequentially:

  1. Skull Stripping (test)
  2. Skull Stripping (process)
  3. Template Registration (test)
  4. Template Registration (process)
  5. Labelling
  6. 2D Conversion

run_image_processing.sh / run_image_processing.bat

Runs all image processing substages sequentially:

  1. Center Crop
  2. Image Enhancement
  3. Data Balancing

run_full_pipeline.sh / run_full_pipeline.bat

Runs all stages in sequence:

  1. Environment Setup
  2. Data Preparation
  3. NIfTI Processing (all substages)
  4. Image Processing (all substages)

Warning: This will take several hours and requires significant computational resources.

Prerequisites

Before running any script:

  1. Python 3.10+ must be installed
  2. Dependencies should be installed (pip install -r requirements.txt)
  3. Configuration files should be set up (see configs/default.yaml)
  4. Template files should be downloaded (see support_files/templates/*/README.md)

Usage Tips

For Non-Technical Users

  • Start with individual stage scripts
  • Run stages one at a time
  • Check outputs between stages
  • Monitor system resources (RAM, disk space)

For Advanced Users

  • Use full pipeline script if you have powerful hardware
  • Can leave running unattended
  • Monitor logs in .reports/ directory

Troubleshooting

Scripts won't execute (Unix/Linux/macOS)

Make scripts executable:

chmod +x scripts/unix_based_system/*.sh

Python not found

Ensure Python is in your PATH:

# Check Python version
python --version

# Or try python3
python3 --version

Script fails with error

  • Check that you're in the project root directory
  • Verify configuration files are set up correctly
  • Check that required template files are downloaded
  • Review error messages in the terminal output

Alternative: Direct Python CLI

If you prefer more control or need to customize parameters, you can run the Python CLI directly:

adp <stage> <action> [options]

See the main README.md for detailed CLI usage examples.