From 8cd8effaa8374545f594768b35b0a3cd42c9e4d6 Mon Sep 17 00:00:00 2001 From: malteekj <44469884+malteekj@users.noreply.github.com> Date: Wed, 5 Jun 2024 10:20:56 -0700 Subject: [PATCH] Update README.md for aortic calcium --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index d73b165..90799be 100644 --- a/README.md +++ b/README.md @@ -83,10 +83,11 @@ bin/C2C spine -i ### Usage ```bash -bin/C2C aortic_calcium -i +bin/C2C aortic_calcium -i -o --threshold ``` -- input_path should contain a DICOM series or subfolders that contain DICOM series, or a nifti file. -- Aortic calcifications are detected through an adaptive threshold in a dilated aorta mask +- The input path should contain a DICOM series or subfolders that contain DICOM series, or a nifti file. +- The threshold can be controlled with --threshold and be either an integer HU threshold, "adataptive" or "agatson". + - If "agatson" is used, agatson score is calculated and the a threshold of 130 HU is used - Aortic calcifications are divided into abdominal and thoracic at the T12 level - Segmentation masks for aortic calcium, the dilated aorta mask and the T12 seperation plane are saved in ./segmentation_masks/ - Metrics on an aggregated and individual level for the calcifications are written to .csv files in ./metrics/