From f32135988984799a0258c613682b8197ab3a81a5 Mon Sep 17 00:00:00 2001 From: Andras Lasso Date: Thu, 21 Jul 2022 09:42:35 +0200 Subject: [PATCH] Add note on graphical user interface in 3D Slicer --- readme.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/readme.md b/readme.md index 58f0ead..9e5cf10 100644 --- a/readme.md +++ b/readme.md @@ -26,7 +26,14 @@ coefficient and -0.80 to -2.75 mm for the Hausdorff distance (Bonferroni-adjuste - HD-BET is very fast on GPU with <10s run time per MRI sequence. Even on CPU it is not slower than other commonly used tools. -## Installation Instructions +## Graphical user interface + +HD-BET is available with a convenient graphical user interface in [3D Slicer](https://www.slicer.org) via the [HDBrainExtraction](https://github.com/lassoan/SlicerHDBrainExtraction#hdbrainextraction) extension. It can be installed with a few clicks as described [here](https://github.com/lassoan/SlicerHDBrainExtraction#tutorial) (in this case it is *not needed* to follow the steps described in "Installation Instructions" section below). + +![Screenshot of HD-BET in 3D Slicer](https://github.com/lassoan/SlicerHDBrainExtraction/raw/main/Screenshot01.jpg) + +## Installation Instructions + Note that you need to have a python3 installation for HD-BET to work. Please also make sure to install HD-BET with the correct pip version (the one that is connected to python3). You can verify this using the `--version` command: