Tutorial

How to calculate maps with TomatoExe?

TomatoExe is a command line tool that allows for map calculation and saving in a DICOM format. To specify the input DICOM files and the settings of map calculation, a yaml file is used as an input. For a detailed Tomato yaml description, see how to work with yaml files.

How to calculate a map - step by step guide

Download TomatoExe for your operating system from here: https://github.com/MRKonrad/tomato/releases/latest. See the discussion about Tomato OpenSource and Full version here.
Download testData.zip from here: https://github.com/MRKonrad/tomato/releases/latest.
Unzip the downloaded files.
Prepare a yaml configuration file, for example by modifying the ones provided in testData.zip, or generate your own one like myTomatoConfigFile.yml. For details on how to use yaml in Tomato please see the section about working with yaml files.
Using command line, navigate to the directory with TomatoExe file

Run TomatoExe

on OSX or Linux
```
./TomatoExe myTomatoConfigFile.yml
```
on Windows
```
TomatoExe.exe myTomatoConfigFile.yml
```

The maps have been generated in the output directory specified in myTomatoConfigFile.yml.
See the maps using your favourite DICOM browser, for example http://www.microdicom.com/ for Windows or https://horosproject.org/ for OSX.
Enjoy 🍅🍅🍅

How to calculate a map - a video guide

A YouTube tutorial can be found here https://www.youtube.com/watch?v=0tzNZNiZh18

Examples of scenarios when Tomato can be used

when the maps are not generated automatically on the scanners
when vendors change the algorithm with which the automatically generated maps have been calculated
when one wants to calculate maps with different algorithms or parameters than these from the scanner
when one wants to generate R2, SNR or SD maps
when one wants to ensure that the same algorithm was used to calculate results in their whole study.