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CEST User Manual
Updated 2 Days AgoPublic

Getting Started

How to install MITK CEST preview

Download

NOTE: Currently we provide the preview version for Linux and Windows. The official releases will also support MacOS like the normal MITK Worbench releases.

You can find the MITK CEST package here: http://www.mitk.org/download/CEST-Preview/2020-07-21/
Pick your system and download it.

Installation and start

To install MITK CEST unpack the package into a directory of your choice.

Starting MIKT CEST under Windows:

  • start MitkWorkbench.exe in the directory <your_unzipped_install_dir>\bin
NOTE: Your first start up may take several minutes (depending on the performance of your system and your drive, as all the plugin DLLs and there dependencies have to been loaded and indexed , so be please wait... it is worth it ;). Following startups become much faster...

Starting MIKT CEST under Linux:

  • start MitkWorkbench.sh in the directory <your_unzipped_install_dir>

How to prepare your data

Folder structure

The most easiest way to properly load your CEST data is to sort your CEST data in one individual folder per measurement (i.e. all 2D/3D images for one Z-spectrum in one folder).

CEST specific meta information

There are some information needed to interpret CEST data correctly that is normaly not provided by the DICOM tags. The following section explains how to provide this information in order to load the data correctly

LIST.txt - Frequency offsets Δω

Put one file named LIST.txt in each CEST folder containing a list of the acquired frequency offsets (i.e. line by line) for this CEST image.
Example:

LIST.txt
−300
6
5
4
// [and so on till the last offset]//
-6
NOTE: To specify the reference M0 images used for normalization off follwowing offsets, please type into the list a frequency offset Δω ≤ −300 ppm. You may have multiple M0 images in one list.
CEST_META.json - Additional meta information

You can either specify additional information in the loading process (see below) or store it in file CEST_META.json to automatically load it with the images.
To use this meta file feature, you have to put one file named CEST_META.json per measurement in each folder containing information about the saturation parameters. Currently the following parameters are supported:

  • CEST.B1Amplitude: The RF B1amplitude
  • CEST.DutyCycle: duty cycle DC in [%]
  • CEST.PulseDuration: pulse duration tp in [μs]
  • CEST.MergeAllSeries: Some acquesition setups store each offset image as own series. This results in a splitted/invalid loading of the CEST image, as only the offset associated with the selected file will be loaded. To mitigate this problem you may set option to Yes. This will force MITK to load all files in the directory and merge them into one image. Possible values: Yes | No

Example:

CEST_META.json
{
 "CEST.B1Amplitude": 0.7,
 "CEST.DutyCycle" : 0.8,
 "CEST.PulseDuration" : 20000
}

Instead the parameters can also be specified manually via the pop-up window during data loading File reading options/CEST DICOM Manual Reader. Note: The option Merge all series allows combining images acquired in different measurements but located in the same folder.

Loading your data

You can use the normal means of the MITK workbench to load CEST data (e.g. drag and drop from file explorer or FileOpen File...).
If you provide a CEST_META.json the Workbench will automatically select the CEST DICOM Manual Reader.

If available the information from CEST_META.json are loaded and shown in the dialog. Besides the meta information (see above) you also have the following options:

  • Normalize data: (Default: Automatic; values: Automatic | No) If set to Automatic the data will automatically normalized if a it containes M0 images (M0 images are indicated by special offset values in LIST.txt.

You are also free to choose this reader if you want to configure your dicom reading process manually for CEST evaluation.

CEST Tools

You find all CEST plugins in the CEST ribbon:


Click on the ribbon to expand it and show all plugins:

Explanation for all plugins: under construction. coming soon

Exploring your CEST data

To explore your CEST data you may use two plugins (CEST Statistics and CEST Inspector).


To use them select your CEST data set in the data manager and navigate to the point of interest to show the CEST spectrum at this point.

Coming soon

• Asymmetry analysis
• Lorentzian Fit-based evaluation
• WASABI field mapping

Last Author
kislinsk
Last Edited
Sun, Aug 2, 7:35 AM

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