Guidelines and Experience Using Imaging Biomarker Explorer (IBEX) for Radiomics

Summary

We describe IBEX, an open-source tool designed for medical imaging radiomics studies, and how to use this tool. In addition, some published works that have used IBEX for uncertainty analysis and model building are showcased.

Abstract

Imaging Biomarker Explorer (IBEX) is an open-source tool for medical imaging radiomics work. The purpose of this paper is to describe how to use IBEX's graphical user interface (GUI) and to demonstrate how IBEX calculated features have been used in clinical studies. IBEX allows for the import of DICOM images with DICOM radiation therapy structure files or Pinnacle files. Once the images are imported, IBEX has tools within the Data Selection GUI to manipulate the viewing of the images, measure voxel values and distances, and create and edit contours. IBEX comes with 27 preprocessing and 132 feature choices to design feature sets. Each preprocessing and feature category has parameters that can be altered. The output from IBEX is a spreadsheet that contains: 1) each feature from the feature set calculated for each contour in a data set, 2) image information about each contour in a data set, and 3) a summary of the preprocessing and features used with their selected parameters. Features calculated from IBEX have been used in studies to test the variability of features under different imaging conditions and in survival models to improve current clinical models.

Introduction

In medicine, patient disease diagnosis typically incorporates a large number of diagnostic exams such as x-rays, ultrasound, computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) scans to assist in determining the course of patient care. While physicians use these images to qualitatively assess patient's diagnosis, there may be additional quantitative features that can be extracted to guide patient care. The rationale is that these features may represent proteomic and genomic patterns expressed on the macroscopic scale¹. Combining this quantitative information with the current clinical informatio....

Protocol

1. Install IBEX

NOTE: To install a source-code version go to step 1.1. Alternatively, to install a stand-alone version go to step 1.2.

1. Source-code version
   1. Go to the IBEX source-code version website³. Download the "IBEX_Source.zip" and "How_to_use.pdf" files. Look in the "How_to_use.pdf" file to find the pre-requisites to use the latest IBEX version.
      NOTE: IBEX works only on 32 bit and 64 bit Matlab versions 2011a and 2014b, respectively.
   2. Once the download is completed, unzip the "IBEX_Source.zip" and add the \IBEX_Source folde....

Results

The output from IBEX is a spreadsheet (see Figure 4) that contains 3 tabs. The "Results" tab contains the feature values for each ROI in the data set (Figure 4A). The "Data Info." tab contains information about the images taken from each ROI in the data set (Figure 4B). The "Feature Info." tab contains a comprehensive list of features used with the parameters selecte.......

Discussion

IBEX is a powerful tool for medical imaging radiomics research. It has thus far mostly been used for radiation oncology purposes in studies conducted by the MD Anderson radiomics group. IBEX allows for manipulation of ROIs and calculation of features within 5 main feature categories. The source code version of IBEX allows the user to design applications that are not already part of IBEX, such as gray level zone matrix features.

The main steps involved in IBEX are the import of images, contouri.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Excel	Microsoft Office		Any version of excel should work.
Matlab	MathWorks		Only use IBEX on 32 bit Matlab 2011a or 64 bit Matlab 2014b.