CrCEST

CrCEST processing GUI

This MATLAB GUI is designed to process CrCEST imaging data by generating quantitative maps of creatine recovery and exchange. Users can load raw image datasets, define regions of interest, perform voxel-wise fitting, and apply both B₀ and B₁ correction. The software was developed and tested using MATLAB R2024 and includes integrated support for analyzing exercise-recovery datasets. Here is a tutorial video to implement or better understand CrCEST imaging in a practical setting.

The code is available on GitHub: https://github.com/newilson/ExerciseCESTv2

Description

ImScribe is designed to allow reproducible selection of the same anatomical Field-of-View in Siemens MRI studies. The program is written in Matlab and requires the installation of the SPM software toolbox (see Requirements below). It is specifically intended for group studies in neuroimaging applications (like fMRI) where reproducible acquisition of the same anatomical brain region is desired. The program is specific to the Siemens Dicom imaging format and method of specifying imaging FOVs.

Procedure

Described in the CrCEST Tutorial Video.

Features

  • Designed for use with exercise-recovery studies involving dynamic CrCEST acquisition

  • Supports processing of single-slice, multi-slice, and 3D CrCEST datasets

  • Works directly with Siemens DICOM images

  • Performs voxel-wise CrCEST fitting with integrated B₀ and B₁ correction

    • Default B₀ correction uses the WASSR method

    • Default B₁ correction applies a linear scaling approach

  • Allows ROI-based analysis using user-defined or dice-based masks

  • Outputs quantitative maps of creatine signal recovery and CrCEST recovery time for each defined ROI

  • Provides visual feedback on signal quality, ROI placement, and fitting results

Requirements
  • MATLAB 2019 (or newer).
Installation Instructions
  • Download the software from GitHub (see Download section below).
  • Add your local folder to your Matlab Path.
  • Run Matlab and type ExerciseCESTv2 at the prompt to bring up the CEST GUI.
Downloading

The ImScribe program is available on GitHub: https://github.com/newilson/ExerciseCESTv2

Contact

For comments or questions on the CrCEST analysis program, contact Ryan Ambruster.