Using the wolfram engine

Script based segmentation without mathematica

simple, fast and reliable

Everything 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 on the github page.

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 the latest version of QMRITools for the Wolfram engine using the Install_QMRITools.wls WolframScript.

wolframscript -f "path to file\Install_QMRITools.wls"

To install an other version of the QMRITools from the GitHub release pages use

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

Segmentation script

To see how to use the script run:

wolframscript -script "path to file\Segment_Nii.wls" --h

Use -script and not -f, wolframscript -f does not pass arguments starting with - to the script. This will give the up to data help that might change over time, currently it is:

Usage:
  script.wls --i <input> [--o <output>] [--g Y|N] [--l <region>]
Flags:
  --i    Input NIfTI file (required)
  --o    Output NIfTI file (default: <input>_seg.nii(.gz))
  --g    Use GPU? (Y/N, default: N)
  --l    Region to segment (default: Body), one of:
         <list of all regions, keys of $SegmentationLabels>
  --h, --help  Show this help message

The default region Body segments the full body with the full body muscle labels. The regions Legs, LegsHip, UpperLegs, LowerLegs, Hip, Shoulder and Arm give the older labels files, the other regions give the full body labels. The labels file is written next to the output file.

Run the segmentation script (works on in or out phase data, raw echo data, water or fat reconstruction):

wolframscript -script "path to file\Segment_Nii.wls" --i "file to be segmented.nii.gz" --o "output file.nii"

It does not matter which body region is in the data (the region is detected automatically) and if one or two legs are in the field of view. To segment a specific region add for example --l UpperLegsBody. For the situation where you run the scrip from its own folder with the test folder also there this will be script.

wolframscript -script "Segment_Nii.wls" --i "test data\test_up.nii.gz" --o "test data\out_up.nii"

wolframscript -script "Segment_Nii.wls" --i "test data\test_low.nii.gz" --o "test data\out_low.nii"

By default the CPU is used, to use the GPU add --g Y.

We gratefully acknowledge the support of NVIDIA with the donation of the GPU used for this work.