Using the wolfram engine

Script based segmentation without mathematica

simple, fast and reliable

Everyting in QMRITools can also run from the command line using the Wolfram engine. For segmentation there are dedicated scripts that install and run the segmentation software. Below is a short manual on how to use these tools. The scripts and so example data can be found here.

Wolfram engine and script

Install the free Wolfram Engine as described here:

https://www.wolfram.com/engine/ https://support.wolfram.com/45743

Install WolframScript as described here

https://reference.wolfram.com/language/workflow/InstallWolframScript.html

QMRITools

Install QMRITools for the worlfram enging using the Install_QMRITools.wls WolframScript.

The latest release link needed for the command line command can be found on the releases page.

wolframscript -f "path to file\Install_QMRITools.wls" https://github.com/mfroeling/QMRITools/releases/download/4.x.x/QMRITools-4.x.x.paclet

For the situation where you run the scrip from its own folder with the test folder also there this will be script

wolframscript -f "Install_QMRITools.wls" https://github.com/mfroeling/QMRITools/releases/download/4.x.x/QMRITools-4.x.x.paclet

Segmentation script

Run the segmentation script (networks are currelty for out-phase dixon data):

wolframscript -f "path to file\Segment_Nii.wls" "file to be segmented.nii.gz" "output file.nii"

For the situation where you run the scrip from its own folder with the test folder also there this will be script

wolframscript -f "Segment_Nii.wls" "test data\test_up.nii.gz" "test data\out_up.nii"

wolframscript -f "Segment_Nii.wls" "test data\test_low.nii.gz" "test data\out_low.nii"

By default the CPU is used, if you want to switch to GPU open the script in any text editor and change “CPU” for “GPU”.