====== CEST data evaluation tool======
{{ :cest_eval.png?direct&200|}}
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

Dowload zipped Matlab implementations [[https://github.com/cest-sources/CEST_EVAL/archive/master.zip|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. [[http://onlinelibrary.wiley.com/doi/10.1002/nbm.3054/|doi: 10.1002/nbm.3054]]**. 

Fitting: **Windschuh et al. (2015), NMR Biomed., 28(5):529-37.  [[http://onlinelibrary.wiley.com/doi/10.1002/nbm.3283/abstract|doi: 10.1002/nbm.3283]]**. 

WASABI B1/B0 mapping and correction: **Schuenke et al. (2016), MRM [[http://onlinelibrary.wiley.com/doi/10.1002/mrm.26133/abstract|doi: 10.1002/mrm.26133]]**. 

===== 1/2 Basic Z-spectra evaluation =====
{{youtube>4aA1D2A60Og?500x360|Tutorial: 10 minutes for basic CEST evaluation}}

===== 2/2 Lorentzian fitting for isolated CEST evaluation =====
{{youtube>NxCXS5_X3yk?500x360|Tutorial: 10 minutes for basic 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 John Hopkins group here 

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


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