=Getting Started
== How to prepare your data
=== {icon folder-open} 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).
=== {icon info-circle} 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:
−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:
lang=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.
== {icon upload} 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 {nav File > Open File...}).
If you provide a `CEST_META.json` the Workbench will automatically select the `CEST DICOM Manual Reader`.
{F1667978}
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.
= Coming soon
• Asymmetry analysis
• Lorentzian Fit-based evaluation
• WASABI field mapping