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--- cest_eval [2016/02/14 14:22]
+++ cest_eval [2020/07/23 12:30]
mzaiss
@@ Line 1: / Line 1: @@
+====== 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/]]
+{{ :logo_dkfz.png?direct&180|powered by DKFZ}}

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