CEST sources
Welcome to CEST sources! CEST stands for Chemical Exchange Saturation Transfer, a Magnetic Resonance Imaging (MRI) technique which promises insight into pathologies on a molecular level. If you want to know more about CEST, find details in the CEST intro or the reviews. CEST sources is a project to share code, link resources, and bundle knowledge about CEST. CEST sources is intended for helping researchers and students in the field of CEST and magnetization transfer. Most code is in Matlab but we try to upload other implementations, too.
Overview
Find below the different sections of CEST sources. For now the focus is on Z-spectra evaluation methods, and Z-spectra simulation and fitting. Each subsection contains links to code and video tutorials. All code is kept simple to be easily adjustable for your scientific question. If you have a suggestion for a video tutorial feel free to contact us.
Download links to all packages can be found on the github page github.com/cest-sources. (About github)
1. Data evaluation tools
1.1 Image data preprocessing - Normalization, B0 correction, Lorentzian fitting, and contrast computation
1.2 Z-spectra B1-correction
Correction for B1 inhomogeneity artifacts in CEST images
1.3 Pulseq-CEST evaluation examples
The Pulseq-CEST library shares short MATLAB and Python scripts that evaluate data from a matching Pulseq-CEST sequence, including MTRasym, multi-pool Lorentzian difference, T1, T2, and WASABI. The scripts are in eval-examples. The library and these evaluations are described in The Pulseq-CEST Library: definition of preparations and simulations, example data, and example evaluations.
2. Analytical solutions of the Bloch-McConnell equations
Here you find Z-spectrum simulations in the case of a two and three pool systems under continuous wave (cw) irradiation. For a two pool system also the solution for pulsed spinlock irradiation is given.
Analytical solution for 2-pools under cw irradiation
Analytical solution for 3-pools under cw irradiation: water, CEST and semi-solid MT
Analytical solution for 2-pools under pulsed spin-lock irradiation (ISAR2)
3. Full numerical solutions of the Bloch-McConnell equations
3.1 Full numerical Bloch-McConnell solution
Full numerical Bloch-McConnell solution
3.2 Pulseq-CEST
Pulseq-CEST has simulation codes integrated and linked on the project site.
4. Quantitative CEST
Here you find methods for CEST quantification. This means to achieve access to the CEST pool parameters as defined in the Bloch-McConnell equations such as exchange rate, concentration and transverse relaxation of the CEST site.
CEST quantification by a Multi-B1-fit under cw irradiation - 2 pools
5. CEST Theory
Here you find some Mupad codes for getting more theoretical insight into the eigenspace solution that forms the analytical CEST solution.
Bloch, Bloch-McConnell, and CEST-Theory
6. standard CEST protocols
For reproducible CEST we need to agree on some standard protocols. Find a collection of used sequences here. standard CEST protocols
7. CESTineers - CEST on a Siemens platform
CESTineers is a resource for CEST MRI on a Siemens platform: available sequences, tested protocols, and notes on post-processing.
8. Literature
CEST sources was initiated 2014 at the German Cancer Research Center (DKFZ), Heidelberg Germany by the project group CEST imaging.
It was then hosted at Max Planck Institute for Biological Cybernetics, Tübingen and part of the european GLINT project.
It is now hosted at the Professur für multimodale Bildgebung in der klinischen Forschung of Prof. Dr. rer. nat. Moritz Zaiss, Neuroradiologisches Institut, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg.
If you want to publish or link to code here, too, feel free to contact us.