CEST data evaluation tool

This tool allows you to evaluate CEST MRI data and create CEST images and ROI evaluations from basic contrasts as well as sophisticated multi-Lorentzian fits

Download zipped Matlab implementations here or find the package on https://github.com/cest-sources/CEST_EVAL/

Tutorial

These routines allow you to

import raw data
Calculate B0 maps from Z-spectra
B0 correct Z-spectra
investigate CEST spectra for pixels and ROIs
calculate contrasts (MTRasym, MTRRex, Lorentzian difference, AREX)
fit multi-Lorentzian fits to Z-spectra

MTRRex,AREX: Zaiss et al. NMR Biomed., 27: 240–252. doi: 10.1002/nbm.3054.

Fitting: Windschuh et al. (2015), NMR Biomed., 28(5):529-37. doi: 10.1002/nbm.3283.

WASABI B1/B0 mapping and correction: Schuenke et al. (2016), MRM doi: 10.1002/mrm.26133.

1/2 Basic Z-spectra evaluation

2/2 Lorentzian fitting for isolated CEST evaluation

There are 4 important inputs:

M0_stack(x,y,z) the thermal M0 magnetization, or the normalization image w/o saturation
Mz_stack(x,y,z,w) the stack of saturated images at frequency w
dB0_stack_int(x,y,z) the internal dB0 map in ppm calculated by the minimum of Mz_stack
dB0_stack_ext(x,y,z) an external dB0 map in ppm

further we need the frequency offset axis, or the omega-axis (w-axis) of the Z-spectrum. It is saved in the parameter struct P under the sequence parameters P.SEQ

P.SEQ.w

To calculate the internal B0 map the function MINFIND_SPLINE_3D is called after that the B0-correction and normalization can be performed and the final stack is

Z_corrExt - the B0-corrected and normalized stack of Z-spectra

Alternatives

MITK

The Medical Imaging Interaction Toolkit (MITK) is a free open-source software system for development of interactive medical image processing software. MITK combines the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) with an application framework. As a toolkit, MITK offers those features that are relevant for the development of interactive medical imaging software covered neither by ITK nor VTK, see the Toolkit Features for details. It recently got an extension for CEST analysis MITK CEST:

https://phabricator.mitk.org/w/mitk/cest/cest_user_manual/

JHU

find the CEST data processing tool of the Johns Hopkins group here

http://godzilla.kennedykrieger.org/CEST/