129Xenon Image Processing Pipeline (XIPline)

XIPline application is developed at the CPIR.

Table of contents:

1. Running the Application

2. Usage

3. Acknowledgments

4. Updates

Setup

Standalone Mode

Due to ongoing improvements and updates, we encourage users to run the application in developer mode. If you prefer to use the application as a standalone executable, please contact the authors to obtain the XIPlineInstaller.exe installer.

Developer Mode (Recommended)

To customize the application, the user will need MATLAB version R2023b or newer.

Clone XIPline to your local directory.

git clone https://github.com/aboodbdaiwi/XIPline.git

Start by adding the local folder in the MATLAB path and execute the XIPline.mlapp file.

When implementing new features, or debugging, we recommend using the debugging MATLAB script XIPline_Code_Script.m. This script can run the entire application but without the graphical user interface (GUI).

Set up XIPline folder

1. Download the XIPline folder.

2. Unzip the folder and place it directly in the C:\ drive without renaming or moving it.

3. This directory includes all required components:

   • AI segmentation models
   • Offline reconstruction scripts

These components are essential for image reconstruction, registration, and segmentation.

For GE Data: Waveform Files

Add waveform files in the C:\XIPline\GE\waveforms folder. Please refer to User_Manual.pdf document for more detailed steps.

Usage

These are a few analysis demos (please refer to the user's manual for step-by-step guide on performing all analysis)

1 - Installation demo (Please refer to the instructions above for the latest version)

2 - Calibration Analysis demo

3 - Ventilation Analysis demo

4 - Diffusion Analysis demo

5 - Gas Exchange Analysis demo

6 - Developer Mode demo

Acknowledgments:

Author: Abdullah S. Bdaiwi

Work email: abdullah.bdaiwi@cchmc.org

Personal email: abdaiwi89@gmail.com

Website: CPIR

If you use this software, please cite:

Bdaiwi AS, Willmering MM, Plummer JW, et al. 129Xe Image Processing Pipeline: An open-source, graphical user interface application for the analysis of hyperpolarized 129Xe MRI. Magn Reson Med. 2024;1–18. https://doi.org/10.1002/mrm.30347

Updates:

Task	Date
Add new ventilation analysis report	July 17, 2025
Add offline reconstruction for 2D spiral Philips ventilation images	July 17, 2025
Add ANTs and manual registration for ventilation analysis	July 17, 2025
Remove Python requirement for AI segmentation models	July 17, 2025
Update AI segmentation models	May 20, 2025