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+ | ====== 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 | ||
+ | |||
+ | Dowload zipped Matlab implementations [[https:// | ||
+ | |||
+ | ====== 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, | ||
+ | |||
+ | Fitting: **Windschuh et al. (2015), NMR Biomed., 28(5): | ||
+ | |||
+ | WASABI B1/B0 mapping and correction: **Schuenke et al. (2016), MRM [[http:// | ||
+ | |||
+ | ===== 1/2 Basic Z-spectra evaluation ===== | ||
+ | {{youtube> | ||
+ | |||
+ | ===== 2/2 Lorentzian fitting for isolated CEST evaluation ===== | ||
+ | {{youtube> | ||
+ | |||
+ | There are 4 important inputs: | ||
+ | * **M0_stack(x, | ||
+ | * **Mz_stack(x, | ||
+ | * **dB0_stack_int(x, | ||
+ | * **dB0_stack_ext(x, | ||
+ | |||
+ | 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** | ||
+ | |||
+ | |||
+ | ====== 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:// | ||
+ | |||
+ | |||
+ | |||
+ | ===JHU=== | ||
+ | find the //CEST data processing tool// of the John Hopkins group here | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | |||
+ | {{ : | ||