129Xenon Image Processing Pipeline (XIPline)

XIPline application is developed at the CPIR.

Table of contents:

1. Setup

2. Usage

3. Acknowledgments

Setup

Run Standalone Application

To install XIPline, download the XIPlineInstaller.exe file. and fellow the normal instllation steps. This step doesn't require additional steps except downloading the pre-trained deep-learning models for auto-segmentation (see below).

auto-segmentation: Downloading the .h5 models for machine learning

1 - Download the h5 models for auto segmentation from here.

2 - Create this path C:\XIPline\models in your local C:\ drive and add the downloaded .h5 files in the models folder.

3 - Install Python 3.10.2 and make sure to add the Python path to the environment variables.

Please refer to User_Manual.pdf document for more detailed steps.

For GE Data: Waveform Files

1 - Create this path C:\XIPline\GE_WFs (in the same folder above) in your local C:\ drive and add text files with the names (cal_wf_freq.txt, cal_wf_tr.txt, vent_wf.txt, diff_wf.txt, diss_wf_freq.txt) in the GE_WFs folder.

2- Add the path to the waveform file in the first line of each file. Note: the waveform files should be .mat for vent_wf and diff_wf and .fdl for the rest.

Please refer to User_Manual.pdf document for more detailed steps.

Run Developer Mode

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).

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

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

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