PETMAT: PET Image Preprocessing in MATLAB

PETMAT is a MATLAB-based app designed to facilitate the preprocessing of Positron Emission Tomography (PET) images using the Statistical Parametric Mapping (SPM) toolbox. The app supports operations like smoothing, co-registration, and normalization of PET images and provides an intuitive interface to work with multiple subject datasets.

Features

• Smoothing: Option to smooth the PET images with different Full Width Half Maximum (FWHM) kernels.
• Co-registration: Interpolation options for aligning PET images with anatomical scans.
• Normalization: Rescale images to standard space with interpolation options.
• Multiple subjects: Support for batch processing multiple subjects at once.
• Progress tracking: Real-time completion percentage indicator during the preprocessing.

Installation

1. Clone the repository:

   git clone https://github.com/taha-parsayan/PETMAT.git

2. Open MATLAB and navigate to the directory containing PETMAT.m.

3. Ensure that you have the SPM toolbox installed and added to the MATLAB path. You can download SPM from SPM official website.

4. Run the app by executing:

   app = PETMAT;

Requirements

• MATLAB (R2018b or later recommended)
• SPM12 (must be installed and in the MATLAB path)
• NIfTI PET and anatomical image files

Usage

1. Input: Specify the folder containing the subject PET image files and the subject IDs. PET files should be in NIfTI format (.nii) and the anatomical scan should be named T1.nii.

2. Smoothing Options: Choose the desired level of smoothing for the PET images from the list:

   • No smoothing
   • 5 FWHM
   • 8 FWHM
   • 10 FWHM

3. Co-registration and Normalization: Select the desired interpolation methods for co-registration and normalization processes.

4. Analyze: Click the "Analyze" button to start the preprocessing pipeline.

5. Exit: Close the app by clicking "Exit."

Output

The processed images will be stored in the same subject directories, with names indicating the operation performed:

• coregister_PET.nii: Co-registered PET images
• std_T1.nii: Normalized anatomical scan
• std_coregister_PET.nii: Normalized PET image
• SUV.nii: Standard Uptake Value (SUV) image
• SUV_GM.nii: SUV image masked by gray matter

Contributing

Contributions are welcome! If you encounter any bugs or have feature suggestions, feel free to open an issue or submit a pull request.

Acknowledgments

This app utilizes the SPM toolbox, developed by the Wellcome Centre for Human Neuroimaging. For more information, visit the SPM website.

Citation

If you use this tool in your work, please cite it as:

Mohammadtaha Parsayan, Poul Flemming Høilund-Carlsen, Farzin Kamari, Abass Alavi, Sasan Andalib. PETMAT: A MATLAB-based PET Image Processing Tool. Version 2024-10. [cited (date)] . Available at: https://github.com.mcas.ms/taha-parsayan/PETMAT.