Lung CT Segmentation to Identify Consolidations and Ground Glass Areas for Quantitative Assesment of SARS-CoV Pneumonia

Summary

The aim of this protocol is to provide a time efficient way to segment volumes of interest on high-resolution CT scans to use for further radiomics analysis.

Abstract

Segmentation is a complex task, faced by radiologists and researchers as radiomics and machine learning grow in potentiality. The process can either be automatic, semi-automatic, or manual, the first often not being sufficiently precise or easily reproducible, and the last being excessively time consuming when involving large districts with high-resolution acquisitions.

A high-resolution CT of the chest is composed of hundreds of images, and this makes the manual approach excessively time consuming. Furthermore, the parenchymal alterations require an expert evaluation to be discerned from the normal appearance; thus, a semi-automatic approach to the segmentation process is, to the best of our knowledge, the most suitable when segmenting pneumonias, especially when their features are still unknown.

For the studies conducted in our institute on the imaging of COVID-19, we adopted 3D Slicer, a freeware software produced by the Harvard University, and combined the threshold with the paint brush instruments to achieve fast and precise segmentation of aerated lung, ground glass opacities, and consolidations. When facing complex cases, this method still requires a considerable amount of time for proper manual adjustments, but provides an extremely efficient mean to define segments to use for further analysis, such as the calculation of the percentage of the affected lung parenchyma or texture analysis of the ground glass areas.

Introduction

In the current year, the world is facing a health emergency, the pandemic caused by the novel Coronavirus, Sars-CoV2. Even if, up to the present date, many aspects regarding the physiopathology of the COVID-19 infection are still unclear, it shares several characteristics with its “ancestors” SARS1 and MERS. In particular, it has been proven that the virion spike proteins interact with the Angiotensin Converting Enzyme Type-2, a receptor well represented on the alveolar endothelial cells, but ubiquitous in the human organism, thus having the potentiality to give systemic symptoms¹.

For diagnosis, the curr....

Protocol

This protocol follows the guidelines of the institutional human research ethics committee.

1. Downloading the DICOM images

1. Download the DICOM images and transfer them in the workstation dedicated to the segmentation, with the 3D software installed. If planning to work on a personal computer, anonymize the DICOM data.

2. Importing the HRCT study on the 3D Slicer software

1. In the software opening screen (corresponding to the Welcome to Slicer section in the drop-down menu) select Load DICOM Data. Alternatively, select ....

Results

The proposed method has been refined through trials and errors, testing it on 117 patients affected by COVID-19 pneumonia with a positive rt-PCR test.

After a short learning curve, the time needed to obtain the segments can vary from 5 to 15 minutes, depending on the presentation pattern.

As shown on Figure 1, the method yields precise segments: this can be observed by noticing the exact correspondence with the HRCT. The 3D rendering helps to assess.......

Discussion

Segmentation represents a fundamental step for performing modern quantitative radiology studies, and is necessary to apply radiomics or texture analysis techniques. Pathological findings in the lungs represent one of the most challenging to segment, for the lack of defined anatomical borders and a small difference in attenuation value when compared to the healthy areas.

The source images must present with a minimum of artifacts if possible, especially on the pathological areas, and this is som.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
CT Scanner	General Electrics Healthcare	64-MDCT VCT lightSpeed	The CT scanner used for HRCT acquisitions
Desktop Computer	ThinkCentre		The computer used to download the DICOM files and run 3D Slicer