Journal of Digital Imaging https://doi.org/10.1007/s10278-019-00239-7 Comprehensive Review of 3D Segmentation Software Tools for MRI Usable for Pelvic Surgery Planning Alessio Virzì1,2 & Cécile Olivia Muller2,3 & Jean-Baptiste Marret2,3 & Eva Mille2,3 & Laureline Berteloot2,4 & David Grévent2,4 & Nathalie Boddaert2,4 & Pietro Gori1 & Sabine Sarnacki2,3 & Isabelle Bloch1,2 # Society for Imaging Informatics in Medicine 2019 Abstract Patient-specific 3D modeling is the first step towards image-guided surgery, the actual revolution in surgical care. Pediatric and adolescent patients with rare tumors and malformations should highly benefit from these latest technological innovations, allowing personalized tailored surgery. This study focused on the pelvic region, located at the crossroads of the urinary, digestive, and genital channels with important vascular and nervous structures. The aim of this study was to evaluate the performances of different software tools to obtain patient-specific 3D models, through segmentation of magnetic resonance images (MRI), the reference for pediatric pelvis examination. Twelve software tools freely available on the Internet and two commercial software tools were evaluated using T2-w MRI and diffusion-weighted MRI images. The software tools were rated according to eight criteria, evaluated by three different users: automatization degree, segmentation time, usability, 3D visualization, presence of image registration tools, tractography tools, supported OS, and potential extension (i.e., plugins). A ranking of software tools for 3D modeling of MRI medical images, according to the set of predefined criteria, was given. This ranking allowed us to elaborate guidelines for the choice of software tools for pelvic surgical planning in pediatric patients. The best-ranked software tools were Myrian Studio, ITK-SNAP, and 3D Slicer, the latter being especially appropriate if nerve fibers should be included in the 3D patient model. To conclude, this study proposed a comprehensive review of software tools for 3D modeling of the pelvis according to a set of eight criteria and delivered specific conclusions for pediatric and adolescent patients that can be directly applied to clinical practice. Keywords 3D modeling . MRI . Segmentation software . Pelvic surgery Introduction surgeons, and even more pediatric surgeons, do not have ac- cess in routine to these tools. Imaging the pelvis for a 3D Thanks to the advances in medical imaging technologies, es- patient-specific model entails important difficulties. First, the pecially 3D visualization, the surgeon should better under- involved structures are soft and deformable leading to a strong stand the patient’s anatomy, properly counsel the patient, pre- anatomical inter-patient variability. Secondly, simple automat- dict possible complications, choose the surgical approach, and ic tools such as MIP (maximum intensity projection) or direct use image overlay to guide surgery. However, general 3D volume rendering, only based on the intensity of the voxels, are ineffective for the pelvis due to the strong signal heterogeneity, especially in MRI. Hence, dedicated segmenta- * Alessio Virzì tion tools are mandatory to obtain a comprehensive, relevant, [email protected] and useful 3D pelvic model. We here refer to segmentation of a 3D image as the process of assigning a given label to each 1 LTCI, Télécom Paris, Institut Polytechnique de Paris, Paris, France voxel of the image, such that voxels with the same label be- 2 IMAG2 Laboratory, Imagine Institute, Paris, France long to the same anatomical structure. 3 Department of Pediatric Surgery, Paris Descartes University, Hôpital However, most of the available segmentation and 3D Necker Enfants-Malades, Assistance Publique - Hôpitaux de Paris, modeling software tools focus on CT images (e.g., segmenta- Paris, France tion of bones, liver, and vessels) or on brain MRI. 4 Department of Pediatric Radiology, Paris Descartes University, Our research focuses on pelvic malformations and tu- Hôpital Necker Enfants-Malades, Assistance Publique - Hôpitaux de mors in children and adolescents. This anatomical region is Paris, Paris, France J Digit Imaging complex to represent in 3D, especially in children present- running the software tools on different operating systems, ing rare malformations and tumors and whose anatomy in particular Linux, was also analyzed. varies with age. Surgical planning of such challenging sit- The selected software tools and the corresponding releases uations would highly benefit from the 3D segmentation of are listed in Table 1. They are described in Appendix. the structures of interest, providing the surgeon with a patient-specific 3D model or “digital twin” [1–3]. The ad- Description of the Imaging Dataset vantages of the 3D models in daily practice are especially obvious for surgical planning in oncology, allowing the The imaging data used in this study were gathered from 81 surgeon to better understand the spatial relationships be- patients, with a median age of 6 years (3 months 17 years), tween the tumor and the surrounding structures. For affected by pelvic-abdominal tumors or malformations. MRI anorectal malformations, the 3D models of nerves and exams were performed on a 3-T MRI, as part of a standard muscles may also be useful to better describe the anomalies clinical protocol with the addition of two extra sequences: (i) a of the spinal cord and/or muscles frequently associated quasi-isotropic T2-w MRI, acquired in the coronal plane, cho- with such malformations. This should be useful not only sen as reference anatomical sequence for the segmentation to refine the classification of these malformations, but also procedure, and (ii) a diffusion-weighted (DW) MRI, acquired to evaluate the impact of the different types of surgical in the axial plane, necessary to test the tractography approaches and of potential rehabilitation techniques algorithms. (neuromodulation, physiotherapy, etc.). All patients under 5 years of age received sedation with MRI is the gold standard modality for the pelvis in both phenobarbital. No general anesthesia was required. All pa- adults and children and provides also specific imaging se- tients or patient’s parents gave their informed consent accord- quences for several structures such as, for instance, the nerves. ing to ethical board committee requirements (N°IMIS2015- Moreover, MRI does not produce any ionizing radiation, 04). An example of some MRI slices used in this study is which is important for children that will require iterative im- shown in Fig. 1. aging, especially those treated for cancer. Software tools were evaluated on imaging data issued from In this context, our aim was to evaluate existing segmenta- the complete patient’s cohort except for the segmentation time tion software tools for pelvic MRI segmentation. The evalua- criterion, which is highly dependent on the patient’s age and tion was performed according to our requirements in terms of pathology. We have thus chosen two adolescent patients with daily surgical use of 3D modeling of patients with pelvic tu- a normal pelvis anatomy, one female and one male of the same mors and malformations, e.g., with a limited number of image age (to take into account gender variation) to evaluate this processing steps. criterion. Segmentation was performed with all the software We present here the selected software tools and a set of tools for these two referent patients. Finally, in order not to criteria for comparative analysis, and we provide surgeons bias the segmentation time results, T2-w images having both and researchers with guidelines for choosing the best 3D the same acquisition parameters were chosen for these two modeling software according to their needs. patients: echo time TE = 59 ms, repetition time TR = 5716 ms, flip angle FA = 90°, image size 512 × 512 × 208 voxels, and voxel size = 0.74 × 0.74 × 0.70 mm3. Material and Methods DW MRI scans were acquired immediately after the T2-w acquisitions, in order to minimize the potential patient’sdis- Software Tools Selected for Evaluation placement between the two scans. The DW MRI was acquired using a sequence of 25 directions, a b value of 1000, and a This review focuses on the most generally used software voxel size of 1.4 × 1.4 × 4mm3. tools in the medical image community, in particular by radiologists. We only include the software tools equipped Evaluation Criteria with segmentation tools, 3D rendering tools, and that are usable by a non-expert in image processing. All the ana- In order to evaluate the performances of the software tools on lyzed software tools are freely available on the Internet, the segmentation of the pelvic structures in MRI, we except for two commercial software tools currently used established a list of eight criteria: automatization degree, us- at the Imaging Department of the Pediatric Hospital ability, 3D visualization, segmentation time, image registra- Necker-Enfants Malades of Paris. All free software tools tion functionalities, tractography functionalities, supported were tested on a Windows operating system (OS) (CPU at system, and potential addition of plugins. 3.10 GHz, 16-GB RAM, 64-bit OS), except for the OsiriX These criteria were selected during a multi-disciplinary DICOM Viewer that was tested on a Macintosh OS (CPU expert consensus meeting including anatomists, surgeons, at 2.7 GHz, 16-GB RAM, 64-bit OS). The possibility of radiologists, and specialists in image analysis (from a J Digit Imaging Table 1