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cest_eval [2020/06/15 11:53] (current)
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 +====== 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 ======
 +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}}
  
cest_eval.txt · Last modified: 2020/06/15 11:53 (external edit)