From d1bd33cddf87a7063ea673a11c558135ce33d103 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Pedersen?= Date: Mon, 24 Apr 2023 08:34:19 +0200 Subject: [PATCH 1/2] Docs: added custom arguments example in README [no ci] --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 4f07ec3..d0903f1 100644 --- a/README.md +++ b/README.md @@ -33,8 +33,14 @@ lungtumormask input_file output_file # Example lungtumormask patient_01.nii.gz mask_01.nii.gz + +# Custom arguments +lungtumormask patient_01.nii.gz mask_01.nii.gz --lung-filter --threshold 0.3 --radius 3 ``` +In the last example, we filter tumor candidates outside the lungs, use a lower probability threshold to boost recall, and use a morphological smoothing step +to fill holes inside segmentations using a disk kernel of radius 3. + ## [Citation](https://github.com/VemundFredriksen/LungTumorMask#citation) If you found this repository useful in your study, please, cite the following paper: ``` From 22cd1566ea7b1807543edf7266c39231564971e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Pedersen?= Date: Mon, 24 Apr 2023 08:38:53 +0200 Subject: [PATCH 2/2] Docs: resized figs + added space under figs [no ci] --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d0903f1..997399d 100644 --- a/README.md +++ b/README.md @@ -8,8 +8,11 @@ This is the official repository for the paper [_"Teacher-student approach for lu A pretrained model is made available in a command line tool and can be used as you please. However, the current model is not intended for clinical use. The model is the result of a proof-of-concept study. An improved model will be made available in the future, when more training data is made available. -![sample of masked output](https://github.com/VemundFredriksen/LungTumorMask/releases/download/0.0.1/sample_images.png "Sample output of two different tumors") -![sample of 3d render](https://github.com/VemundFredriksen/LungTumorMask/releases/download/0.0.1/sample_renders.png "3D render of two masked outputs") + + + + +  ## [Installation](https://github.com/VemundFredriksen/LungTumorMask#installation)