# A Prostate MRI Segmentation Tool Based on Active Contour Models Using a Gradient Vector Flow
## 2 Materials and Methods
### Database and ROIs References  
A database with prostate MRI, based on clinical data with tumor and healthy cases was used. The examinations used in our study contained three-dimensional T2-weighted fast spin-echo (TR/TE/ETL: 3600 ms/143 ms/109, slice thickness: 1.25 mm) images acquired with sub-millimetric pixel resolution in an oblique axial plane. Each study comprises a set of 64 slice images. This database was used in previous works [11] and it has been facilitated for testing the software.  
The ground truth annotations were performed using the ProstateAnalyzer tool [11], that allows the drawing of an annotation in a given MRI. For this task, experts with more than 10 years of experience on prostate imaging were asked to provide the annotations using the tool. All the dataset and ground truth data are provided from the medical imaging department of the University Hospital of Dijon (France). The institutional committee on human research approved the study, with a waiver for the requirement for written consent, because MRI and MRSI were included in the workup procedure for all patients referred for brachytherapy or radiotherapy.  
The prostate is composed of a peripheral zone (PZ), central zone (CZ), transitional zone (TZ) and an anterior fibromuscular tissue (AFT) depicted in Figure 1. Most cancer lesions occur in the peripheral zone of the gland, fewer occur in the TZ and almost none arise in the CZ. A detailed description of the influence of the prevalence factor risk according the prostate zone is described in [13]. The T2 WI modality was chosen because it provides the best depiction of the prostate's zonal anatomy.  
The PZ represents up to 70% of a normal prostate gland and around 75% of prostate cancers originate in this zone. The CZ represents about 25% of a normal healthy prostate gland in young adults. Even though the frequency of cancers originating here is much lower, they tend to be of the more aggressive type [14]. An example of a real study case provided by the panel visualization of the prostate tool [11] is depicted in Figure 2. All the overlays are annotated with manual drawings made by radiologists. Each region is represented by different colors (CZ in white and PZ in blue) focusing on a tumor area represented in red (Tum). This example shows the importance of making annotations in regions of interest. In this case, a manual segmentation is validated by experts.  
Figure 1: Anatomy of the prostate in (**a**) transversal and (**b**) sagittal planes [11].  
Figure 2: An example of the anatomy (T2 WI) panel visualization of the tool developed in [11] with the ROIs annotated by radiologists.  
Therefore, one of the main motivations of this work is to develop a new tool focused on improving the results of this initial manual segmentation using Active Contour Models (ACM), facilitating the task of the experts.  
In order to attain the above-mentioned goals, we have implemented a novel Graphical User Interface that permits to import, analyze and annotate prostate MR images. The program requires an initial annotation from the user, that does not require to be perfect, and the outcome is an annotation more accurate than the initial one. The modular design of the software allows for integrating segmentation methods as plug-ins or extensions that can be used for testing and clinical purposes. Additionally, this design enables easy performance comparisons between already integrated methods and new methods. In what follows, we will discuss the design of this GUI and subsequently, we will present a study case using three implementations of an ACS model for segmenting the different prostate sections in MR images. It is important to note that this tool and the developed algorithms have not yet been clinically tested and the results presented here represent a proof of concept. However, for the design of the GUI, the expertise and suggestions of clinical experts have been taken into account.