Main Page/SlicerCommunity/2021

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The community that relies on 3D Slicer is large and active: (numbers below updated on July 1st, 2021)



The following is a sample of the research performed in 2021 using 3D Slicer outside of the group that develops it. (Research performed by groups that are also actively developing 3D Slicer is represented in the publication database).


We monitor PubMed and related databases to update these lists, but if you know of other research related to the Slicer community that should be included here please email: marianna (at) bwh.harvard.edu.

Contents

2021

MONAI Expands its Horizons with Healthcare Imaging Annotation

Publication: nVIDIA DEVELOPER 2021 July 19 |

Authors: Prerna Dogra

Institution: nVIDIA Corporation

Abstract: Open-source frameworks like Project MONAI provide a standardized, transparent, and reproducible template for the creation of, and deployment of medical imaged-focused machine learning models, potentiating efforts such as ours. They allow us to focus on investigating novel algorithms and their application, rather than developing and maintaining software infrastructure.  This in turn has accelerated research progress which we are actively translating into tools of practical relevance to the pediatric community we serve.

  • MONAI v0.1 includes:
    • MONAI Label server: REST API server that facilitates communication with the viewer clients i.e. (3D Slicer, OHIF, etc).
    • MONAI Label sample applications that can be adapted to a given clinical task for MR/CT modality including DeepGrow and DeepEdit which are developed by MONAI researchers.
    • With v0.1, we have released a 3D Slicer plugin for MONAI Label to kick start users in the MONAI Label experience
Build AI-Assisted Annotation Models with MONAI Label | YouTube Video

Transcanal Computed Tomography Views for Transcanal Endoscopic Lateral Skull Base Surgery: Pilot Cadaveric Study.

Publication: J Neurol Surg B Skull Base. 2021 Jun;82(3):338-44. PMID: 34026410

Authors: Lubner RJ, Barber SR, Knoll RM, Kempfle J, Lee DJ, Reinshagen KL, Remenschneider AK, Kozin ED.

Institution: Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, USA.

Abstract: Cadaveric temporal bones ( n = 6) from three specimens underwent high-resolution CT (0.625 mm slice thickness). Using three-dimensional (3D Slicer v.4.8, reformatted "transcanal" views in the plane of the external auditory canal (EAC) were created. Axial and coronal reformats were used to compare and measure distances between anatomic structures in the plane of the EAC.

Fusion of Subarachnoid Hemorrhage Data and Computed Tomography Angiography Data Is Helpful to Identify the Rupture Source in Patients With Multiple Intracranial Aneurysms

Publication: Neurosurg Rev. 2021 Jun;44(3):1411-6. PMID: 32506389

Authors: Yao A, Jia L, Li J, Wang B, Zhang J, Xue Z, Zhao K, Zhao Y, You N, Zhang J, Xu B.

Institution: Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China.

Abstract: Determining the rupture source is imperative in patient with aneurysmal subarachnoid hemorrhage (SAH). About one third of SAH cases with multiple intracranial aneurysms cannot be certain of the rupture source according to the hemorrhage pattern. This study aims to identify of the rupture source in patients with multiple intracranial aneurysms by fusing SAH data and computed tomography angiography (CTA) data. This retrospective study included 52 aneurysmal SAH patients with multiple intracranial aneurysms. In the 52 patients, 36 had definitive hemorrhage patterns on computed tomography imaging. And the other 16 patients had non-definitive hemorrhage patterns, which were bewildered for us to determine the ruptured aneurysms. Fusion of SAH data and CTA data was performed to demonstrate the spatial relationship between the SAH with each aneurysm by using the 3D Slicer software. For the patients with definitive bleed patterns, all of the suspected ruptured aneurysms were confirmed to be accurate according to the surgical records. Interestingly, the suspected rupture sources were correct in 14 of 16 patients with non-definitive hemorrhage patterns. For all 52 patients with multiple intracranial aneurysms, the ruptured aneurysms were identified in 50 cases (96.2%). In conclusion, fusion of SAH data and CTA data can precisely demonstrate the spatial relationship between the SAH with each aneurysm, which is helpful to determine the ruptured aneurysm in patients with multiple intracranial aneurysms.

Assessment of Pulp Volume Changes After Surgically Assisted Rapid Palatal Expansion

Publication: J Stomatol Oral Maxillofac Surg. 2021 Jun;122(3):263-6. PMID: 32621998

Authors: Guler AY, Isik BK, Esen A, Menziletoglu D.

Institution: Oral and Maxillofacial Surgery Department, Soke Oral and Dental Health Centre, Aydin, Turkey.

Abstract: Maxillary transverse deficiency is a common skeletal problem. When the patient is younger, it is treated by rapid palatal expansion by using orthodontic appliances. If this fails or the patient is older, which means skeletal growth is completed, surgically aided rapid palatal expansion (SARPE) becomes necessary. In this technique, after the osteotomies have been made, the two maxillary bones are distracted by tooth-borne device. Since a tooth-borne device will apply the distraction forces on the teeth, the pulp volumes may change. Our aim was to investigate the volume changes of the tooth pulps after SARPE in which a tooth-borne device was used. We scanned our database and included 20 patients (7 males and 13 females) aging between 16 and 30 (mean 19.5±3.97) to this retrospective study. All the patients had undergone SARPE surgeries and they had pre-surgery and postconsolidation cone beam computerized tomography (CBCT) images. All the surgeries had been done in similar ways; all the patients had used similar tooth-borne modified acrylic bonded expansion device. We divided the maxillary teeth into three groups: the incisors, the premolars and the molars. We imported the CBCT images of each patient into 3D Slicer software. We calculated volumes of pulps for all maxillary teeth. We compared volumes with paired t test. Statistical significance level was accepted as P< .05. The devices had been left in place between 83 and 179 days including distraction and consolidation periods (mean 121.35±27.83 days). Amount of the expansions varied between 6.03mm and 11.16mm (mean 7.19±1.18mm). We found a statistically significant decrease of the pulp volumes in incisor, premolar and molar teeth (P<.001) between pre-surgery and postconsolidation periods. When using tooth-borne devices in SARPE, their impacts on teeth pulps should also be considered.

Association of Regional White Matter Hyperintensity Volumes with Cognitive Dysfunction and Vascular Risk Factors In Patients With Amnestic Mild Cognitive Impairment

Publication: Geriatr Gerontol Int. 2021 Jun 9. PMID: 34105230

Authors: Hirao K, Yamashita F, Sakurai S, Tsugawa A, Haime R, Fukasawa R, Sato T, Kanetaka H, Umahara T, Sakurai H, Hanyu H, Shimizu S.

Institution: Department of Geriatric Medicine, Tokyo Medical University, Tokyo, Japan.

Abstract: White matter hyperintensities (WMH) obtained by magnetic resonance imaging (MRI) have been reported to promote neurodegeneration and cognitive decline in patients with mild cognitive impairment (MCI). However, little is known about the association between regional WMH (rWMH) and cognitive dysfunction in MCI. We hence investigated the associations between rWMH volumes and cognitive dysfunction in MCI.

PVH and DWMH lesions were outlined by a neurologist, using the semiautomated freeware 3D Slicer, which is a freely available, open-source software package for the visualization, registration, segmentation, and quantification of medical data.

Association Between Tumor Size and Peritumoral Brain Edema in Patients With Convexity and Parasagittal Meningiomas

Publication: PLoS One. 2021 Jun 10;16(6):e0252945. PMID: 34111188 | PDF

Authors: Shin C, Kim JM, Cheong JH, Ryu JI, Won YD, Ko Y, Han MH.

Institution: Department of Neurosurgery, Hanyang University Guri Hospital, Guri, Gyonggi-do, Korea.

Abstract: Peritumoral brain edema (PTBE) is a common complication in meningioma and disruption of the tumor-brain barrier in meningioma is crucial for PTBE formation. To evaluate the association between meningioma size and PTBE, we measured meningioma volumes using the 3D Slicer in patients with convexity and parasagittal meningiomas.

A New Method to Determine the Optimal Orientation of Slim Modiolar Cochlear Implant Electrode Array Insertion

Publication: Ideggyogy Sz. 2021 May 30;74(5-6):191-5. PMID: 34106549

Authors: Horváth B, Perényi Á, Molnár AF, Csanády M, Kiss GJ, Rovó L.

Institution: University of Szeged, Doctoral School of Clinical Medicine, Szeged, Hungary.

Abstract: Our goal was to determine the optimal orientation of insertion of the Slim Modiolar electrode and develop an easy-to-use method to aid implantation surgery. In some instances, the electrode arrays cannot be inserted in their full length. This can lead to buckling, interscalar dislocation or tip fold-over. In our opinion, one of the possible reasons of tip fold-over is unfavourable orientation of the electrode array. Our goal was to determine the optimal orientation of the Slim Modiolar electrode array relative to clear surgical landmarks and present our method in one specified case.

For the measurement, we used the preoperative CT scan of one of our cochlear implant patients. These images were processed by an open source and free image visualization software: 3D Slicer.

Impact of the Craniofacial Surgery Simulation in Anterior Plagiocephaly on Orbits and Oculomotor Muscles: Biomechanical Analysis With a Finite Element Model

Publication: J Craniofac Surg. 2021 May 28. PMID: 34054084

Authors: Dalmas F, Thollon L, Beylerian M, Godio Raboutet Y, David T, Scavarda D, Denis D, Pech-Gourg G.

Institution: Department of Ophthalmology, University Medical Center, Marseille, France.

Abstract: The aim of this study was to show the displacements and strain induced by the supraorbital band advancement during a craniofacial surgery for an anterior plagiocephaly on the orbital bones and the orbital content thanks to a numerical surgical simulation using the finite element method. A three-dimensional (3D) finite element model of a child with an anterior plagiocephaly was entirely created from a tomodensitometry of a patient followed by our Craniofacial Pediatric team. Data of the tomodensitometry were computed with 3D Slicer to re-create the orbit geometry.

Comparing Three-Dimensional Models of Placenta Accreta Spectrum With Surgical Findings

Publication: Int J Gynaecol Obstet. 2021 May 17. PMID: 33998689

Authors: Mulligan KM, Bartels HC, Armstrong F, Immel E, Corcoran S, Walsh JM, McAuliffe F, McParland P, Carroll S, Higgins S, Mahony R, Donnelly J, Geoghegan T, Colleran G, O'Cearbhaill E, Downey P, Brennan DJ.

Institution: UCD School of Medicine, National Maternity Hospital, Dublin, Ireland.

Abstract: Placenta accreta spectrum (PAS) is associated with significant maternal morbidity mainly related to blood loss. Pre-operative planning is aided by antenatal ultrasound and magnetic resonance imaging. We sought to assess whether three-dimensional (3D) models from MR images were accurate when compared with surgical and pathological findings. Digital Imaging and Communications in Medicine files containing MR images with varying severity of PAS (n = 4) were modeled using 3D Slicer.

Structural Failure Sites in Posterior Vaginal Wall Prolapse: Stress 3D MRI-Based Analysis

Publication: Int Urogynecol J. 2021 Jun;32(6):1399-1407. PMID: 33704534

Authors: Chen L, Xie B, Fenner DE, Duarte Thibault ME, Ashton-Miller JA, DeLancey JO.

Institution: Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.

Abstract: We studied three-dimensional stress MRI at maximal Valsalva of 25 women with (cases) and 25 without (controls) posterior vaginal prolapse of similar age and parity. Vaginal wall factors (posterior wall length and width); attachment factors (paravaginal posterior wall location, posterior fornix height, and perineal height); and hiatal factors (hiatal size and levator ani defects) were measured using 3D Slicer 4.3.0® and a custom Python program. Stepwise linear regression was used to assess the relative contribution of all factors to the posterior prolapse size.

Long-Term Stability and Condylar Remodeling After Mandibular Advancement: A 5-Year Follow-Up

Publication: Am J Orthod Dentofacial Orthop. 2021 May;159(5):613-26. PMID: 33712310 | PDF

Authors: Ehardt L, Ruellas A, Edwards S, Benavides E, Ames M, Cevidanes L.

Institution: Department of Orthodontics and Pediatric Dentistry, School of Dentistry, University of Michigan, Ann Arbor, MI, USA.

Abstract: Forty-two patients underwent bilateral sagittal split osteotomies for mandibular advancement using rigid fixation. Cone-beam computed tomography (CBCT) scans were acquired before surgery (T1), immediately after surgery (T2), and at long-term follow-up (T3). The average follow-up period was 5.3 ± 1.7 years after surgery. Anatomic landmark identification on the cone-beam computed tomographies and subsequent quantification of the changes from T1 to T2 and T2 to T3 were performed in ITK-SNAP (version 2.4; itksnap.org) and 3D Slicer v.4.7 software.

The Development of Novel 2-in-1 Patient-Specific, 3D-Printed Laminectomy Guides with Integrated Pedicle Screw Drill Guides

Publication: World Neurosurg. 2021 May;149:e821-e827. PMID: 33540103

Authors: Kanawati A, Rodrigues Fernandes RJ, Gee A, Urquhart J, Siddiqi F, Gurr K, Bailey CS, Rasoulinejad P.

Institution: London Health Science Centre, Victoria Hospital-London, Ontario, Canada.

Abstract: This was a cadaveric study designed to test novel 2-in-1 patient-specific laminectomy guides, with modular removable pedicle screw drill guides. Three-dimensional (3D) printing has not been applied to laminectomy. This cadaveric study tests novel 2-in-1 patient-specific laminectomy guides, with modular removable pedicle screw drill guides. Computed tomography (CT) scans of 3 lumbar spines were imported into 3D Slicer. Spinal models and patient-specific guides were created and 3D printed. The bones were cleaned to visualize and record the under surface of the lamina during laminectomy. Pedicle screws and laminectomies were performed with the aid of patient-specific guides. CT scans were performed to compare planned and actual screw and laminectomy positions.

Creating a Cross-Sectional, CT and MR Atlas of the Pannon Minipig.

Publication: Anat Histol Embryol. 2021 May;50(3):562-71. PMID: 33529429

Authors: Petnehazy O, Donko T, Ellis R, Csoka A, Czeibert K, Baksa G, Zucker E, Repa K, Takacs A, Repa I, Moizs M.

Institution: Medicopus Nonprofit Ltd, Kaposvar, Hungary.

Abstract: The purpose of this study was to create a detailed cross-sectional anatomical reference atlas of the Pannon minipig by correlating good resolution CT and MR images with high quality cross-sectional anatomical images. According to the authors knowledge, no detailed anatomical atlas is available for the minipig.

"...the CT and MR scans were imported to 3D Slicer."

Optimization of Manufacturing Parameters and Tensile Specimen Geometry for Fused Deposition Modeling (FDM) 3D-Printed PETG

Publication: Materials (Basel). 2021 May 14;14(10):2556. PMID: 34069230 | PDF

Authors: Özen A, Auhl D, Völlmecke C, Kiendl J, Abali BE.

Institution: Institute of Material Science and Technology, Technische Universität Berlin, Germany.

Abstract: Additive manufacturing provides high design flexibility, but its use is restricted by limited mechanical properties compared to conventional production methods. As technology is still emerging, several approaches exist in the literature for quantifying and improving mechanical properties. In this study, we investigate characterizing materials' response of additive manufactured structures, specifically by fused deposition modeling (FDM). A comparative analysis is achieved for four different tensile test specimens for polymers based on ASTM D3039 and ISO 527-2 standards. Comparison of specimen geometries is studied with the aid of computations based on the Finite Element Method (FEM). Uniaxial tensile tests are carried out, after a careful examination of different slicing approaches for 3D printing. We emphasize the effects of the chosen slicer parameters on the position of failures in the specimens and propose a simple formalism for measuring effective mechanical properties of 3D-printed structures.


"...this CAD model is converted by software, called a 3D Slicer, to a 3D printing code, where process information is supplied for manufacturing."

The Use of Cochlear-Enhancement Imaging to Predict Hearing Preservation Following Vestibular Schwannoma Removal

Publication: J Neurosurg Sci. 2021 May 3. PMID: 33940784

Authors: Kim WH, Park HH, Ahn SJ, Park M, Hong CK.

Institution: Department of Neurosurgery, Brain Tumor Center, Gangnam Severance Hospital, Yonsei University Health System, Seoul, Republic of Korea.

Abstract: Background: Hearing preservation is challenging for patients after the removal of large vestibular schwannomas (VSs). Here, using preoperative magnetic resonance (MR) imaging, we investigated the significance of cochlear enhancement (CE) for predicting postoperative hearing preservation.

Methods: Between January 2014 and December 2019, 34 VS-patients with serviceable hearing underwent tumor-removal surgery using a retrosigmoid approach. The presence or absence of CE using both T2-weighted and gadolinium-enhanced T1-weighted MR images was assessed in VS patients using the pixel-analysis method. Segmented volumetric analyses were also performed using GrowCut 3D Slicer software.

Manual Versus Semiautomatic Segmentation of Soft-Tissue Sarcomas on Magnetic Resonance Imaging: Evaluation of Similarity and Comparison of Segmentation Times

Publication: Radiol Bras. May-Jun 2021;54(3):155-64. PMID: 34108762 | PDF

Authors: Dionisio FCF, Oliveira LS, Hernandes MA, Engel EE, de Azevedo-Marques PM, Nogueira-Barbosa MH.

Institution: Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo, SP, Brazil.

Abstract: Objective: To evaluate the degree of similarity between manual and semiautomatic segmentation of soft-tissue sarcomas on magnetic resonance imaging (MRI).

Materials and methods: This was a retrospective study of 15 MRI examinations of patients with histopathologically confirmed soft-tissue sarcomas acquired before therapeutic intervention. Manual and semiautomatic segmentations were performed by three radiologists, working independently, using the software 3D Slicer. The Dice similarity coefficient (DSC) and the Hausdorff distance were calculated in order to evaluate the similarity between manual and semiautomatic segmentation. To compare the two modalities in terms of the tumor volumes obtained, we also calculated descriptive statistics and intraclass correlation coefficients (ICCs).

Comparing the Inter-Observer Reliability of the Tada Formula Among Neurosurgeons While Estimating the Intracerebral Haematoma Volume

Publication: Clin Neurol Neurosurg. 2021 May 1;205:106668. PMID: 33962148

Authors: Gong K, Shi T, Zhao L, Xu Z, Wang Z.

Institution: Department of Neurosurgery, The First Affiliated Hospital of Xia'men University, Xia'men, Fujian, China.

Abstract: Objective: To compare the inter-observer reliability among neurosurgeons while estimating the intracerebral haematoma (ICH) volume by the Tada formula and assess its influence on predicting the severity and prognosis of various ICHs.

Methods: We obtained clinical data from 262 consecutive patients with spontaneous ICH. The haematoma volume was independently calculated and compared by 3D Slicer and eight neurosurgeons. The inter-observer reliability was obtained by calculating the intraclass correlation coefficients (ICC) and Cohen's kappa score (kappa), within different shape and volume ICH subgroups.

Post-Discharge Chest CT Findings and Pulmonary Function Tests in Severe COVID-19 Patients

Publication: Eur J Radiol. 2021 May;138:109676. PMID: 33798931 | PDF

Authors: Balbi M, Conti C, Imeri G, Caroli A, Surace A, Corsi A, Mercanzin E, Arrigoni A, Villa G, Di Marco F, Bonaffini PA, Sironi S.

Institution: Department of Radiology, ASST Papa Giovanni XXIII, Bergamo, Italy.

Abstract: COVID-19 patients admitted to our hospital between February 25 and May 2, 2020, were retrospectively included according to the following criteria: (a) COVID-19 defined as severe based on the WHO interim guidance (i.e., clinical signs of pneumonia plus respiratory rate > 30 breaths/min, severe respiratory distress, and/or SpO2 < 90 % on room air); (b) chest radiograph in the acute setting; (c) post-discharge unenhanced chest CT; and (d) post-discharge comprehensive PFT. Imaging findings were retrospectively evaluated in consensus by two readers, and volume of abnormal lung was measured on CT using 3D Slicer software. Differences between demographics, comorbidities, acute radiographic findings, PFT, and post-discharge clinical and laboratory data of patients with normal and abnormal CT findings were assessed by Mann-Whitney or Fisher tests, and the compromised lung volume-PFT association by Pearson correlation after removing possible outliers.

Radiomic Analysis of the Optic Nerve at the First Episode of Acute Optic Neuritis: An Indicator of Optic Nerve Pathology and a Predictor of Visual Recovery?

Publication: Radiol Med. 2021 May;126(5):698-706. PMID: 33392980

Authors: Cellina M, Pirovano M, Ciocca M, Gibelli D, Floridi C, Oliva G.

Institution: Radiology Department, ASST Fatebenefratelli Sacco, Piazza Principessa Clotilde 3, 20123, Milan, Italy.

Abstract: We reviewed imaging and clinical data of 25 patients with a first episode of optic neuritis (ON) (14 females, 11 males; 5 bilateral ON; 7 left ON; 13 right ON). All patients underwent a complete ophthalmological assessment, including visual acuity and RNFL, neurological evaluation, orbits MRI. Segmentation of the optic nerves was performed through 3D Slicer open software to get radiomics analysis. All patients underwent a complete neuro-ophthalmological follow-up at 6 months to assess the VO, classified as: complete recovery, partial recovery, deficit persistence/relapse, or visual worsening and were diagnosed as MS or clinically isolated syndrome.

Novel 3D MRI Technique to Measure Perineal Membrane Structural Changes With Pregnancy and Childbirth: Technique Development and Measurement Feasibility

Publication: Int Urogynecol J. 2021 Apr 24. PMID: 33893825

Authors: Pipitone F, Swenson CW, DeLancey JOL, Chen L.

Institution: Pelvic Floor Research Group, University of Michigan, Ann Arbor, MI, USA.

Abstract: Introduction and hypothesis: We aimed to develop and validate a new MRI-based perineal membrane reconstruction and morphological measurement technique, and test its feasibility on nulliparous and parous women to determine the effects of pregnancy and childbirth on the perineal membrane.

Methods: The perineal membrane was traced on high-resolution MRI using 3D Slicer and analyses performed using Rhinoceros 6.0 SR23®. Validation was done by comparing MRI-based perineal membrane reconstruction to dissection measurements in a cadaver. Feasibility of reconstruction was assessed in the following three groups: nulliparous (NP), primiparous women who underwent cesarean delivery (CD), and primiparous women with vaginal delivery (VD). The following parameters were measured: (1) swinging door angle, (2) bony and (3) soft tissue attachment lengths, (4) separation at perineal body level, (5) surface area, and (6) hiatal area. ANOVA and post-hoc comparisons were performed, and the effect sizes (d) were reported.

Radiomic Machine Learning Classifiers in Spine Bone Tumors: A Multi-Software, Multi-Scanner Study

Publication: Eur J Radiol. 2021 Apr;137:109586. PMID: 33610852

Authors: Chianca V, Cuocolo R, Gitto S, Albano D, Merli I, Badalyan J, Cortese MC, Messina C, Luzzati A, Parafioriti A, Galbusera F, Brunetti A, Sconfienza LM.

Institution: Clinica di Radiologia EOC, Istituto di Imaging della Svizzera Italiana (IIMSI), Lugano, Switzerland.

Abstract: Purpose: Spinal lesion differential diagnosis remains challenging even in MRI. Radiomics and machine learning (ML) have proven useful even in absence of a standardized data mining pipeline. We aimed to assess ML diagnostic performance in spinal lesion differential diagnosis, employing radiomic data extracted by different software.

Methods: Patients undergoing MRI for a vertebral lesion were retrospectively analyzed (n = 146, 67 males, 79 females; mean age 63 ± 16 years, range 8-89 years) and constituted the train (n = 100) and internal test cohorts (n = 46). Part of the latter had additional prior exams which constituted a multi-scanner, external test cohort (n = 35). Lesions were labeled as benign or malignant (2-label classification), and benign, primary malignant or metastases (3-label classification) for classification analyses. Features extracted via 3D Slicer heterogeneityCAD module (hCAD) and PyRadiomics were independently used to compare different combinations of feature selection methods and ML classifiers (n = 19).

Virtual Planning and CAD/CAM-Assisted Distraction for Maxillary Hypoplasia in Cleft Lip and Palate Patients: Accuracy Evaluation and Clinical Outcome

Publication: J Craniomaxillofac Surg. 2021 Apr 21;S1010-5182(21)00105-0. PMID: 33906808

Authors: Gerbino G, Autorino U, Giaccone E, Novaresio A, Ramieri G.

Institution: Division of Maxillofacial Surgery, Città della Salute e della Scienza Hospital, University of Torino, Italy.

Abstract: The aim of this prospective study was to report the experience with a specific guided distraction protocol for the treatment of CLP patients with severe midface hypoplasia. From January 2016 to April 2019, six consecutive, non-growing, CLP patients with maxillary hypoplasia underwent a specific distraction protocol based on the use of VSP, CAD/CAM-generated surgical splints, cutting guides, prebent internal maxillary distractors, early removal of distractors, and acute callus manipulation and fixation. STL files for VSP, using multislice CT scans taken preoperatively (T0) and 3 months after distractor removal (T1) were superimposed using the free software 3D Slicer.

The Topology of Ventricle Surfaces and Its Application in the Analysis of Hydrocephalic Ventricles: A Proof-of-Concept Study

Publication: Neuroradiology. 2021 Apr 15. PMID: 33860336

Authors: Lo YT, Kumar S, Tan LQ, Lock C, Keong NCH.

Institution: Department of Neurosurgery, National Neuroscience Institute, Singapore.

Abstract: Twenty-one patients with NPH were recruited from our institution, and 21 healthy controls (HC) and patients with Alzheimer's disease (AD) were identified from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. On T1-weighted fine-cut magnetic resonance sequences, 3D Slicer was used to segment the left frontal horn.

Wearable Mixed-Reality Holographic Navigation Guiding the Management of Penetrating Intracranial Injury Caused by a Nail

Publication: J Digit Imaging. 2021 Apr 12. PMID: 33846887

Authors: Li Y, Huang J, Huang T, Tang J, Zhang W, Xu W, Wang N, Deng Y, Yu X, Xu L.

Institution: Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.

Abstract: Penetrating brain injury caused by a nail is an extremely rare neurosurgical emergency that poses a challenge for neurosurgeons. Nail entering the brain from the orbit and lodging within the cranial cavity is even more unusual. A 53-year-old male was found unconscious at a construction site, and brain CT revealed not only the presence of a nail beneath the inner table of the parietal bone, but also traumatic intracerebral hematoma. Consequently, accurate localization of the nail and hematoma was mandatory for surgical plan. During surgical planning, computational model reconstruction and trajectory calculation were completed using preoperative CT in 3D Slicer.

BreastImplantAnalyzer: An Easy-to-Use, Validated Tool for Calculating Breast Implant Volume From MRI Data

Publication: J Plast Reconstr Aesthet Surg. 2021 Apr 8;S1748-6815(21)00158-3. PMID: 33972201

Authors: Levine L, Kassira W.

Institution: University of Miami Miller School of Medicine, Miami, USA.

Abstract: Given the prevalence of breast augmentation and prosthetic-based breast reconstruction, it is common for the plastic surgeon to see patients presenting for revisional implant surgery. A frequent issue encountered in such procedures is uncertainty of implant size, which presents numerous challenges and may lead to undesired outcomes for both the patient and the surgeon. There is currently no tool available with the purpose of measuring implant volume from magnetic resonance imaging (MRI) data. In this study, such a program was designed and tested.

"...plastic surgeons can easily calculate breast implant volume pre-operatively using BreastImplantAnalyzer, which is available to download for free from www.BreastImplantAnalyzer.com or as an extension for the popular medical imaging platform 3D Slicer.

Application of 3D Modeling and Fusion Technology of Medical Image Data in Image Teaching

Publication: BMC Med Educ. 2021 Apr 6;21(1):194. PMID: 33823845 | PDF

Authors: Yuan Q, Chen X, Zhai J, Chen Y, Liu Q, Tan Z, Chen G, Zhuang K, Zhang J, Xu X, Qiang D, Shao X.

Institution: Department of Imaging, Yi-Ji Shan Hospital, Wannan Medical College, Anhui, China.

Abstract: A total of 460 medical imaging students were selected and randomly divided into two groups. The research group received the teaching of the fusion of the original CT and MR data 3D model and the original image combined with 3D anatomical image. CT and MRI data are imported through load DICOM of 3D Slicer.

Radiomics Analysis for Predicting Pembrolizumab Response in Patients With Advanced Rare Cancers

Publication: J Immunother Cancer. 2021 Apr;9(4):e001752. PMID: 33849924 | PDF

Authors: Colen RR, Rolfo C, Ak M, Ayoub M, Ahmed S, Elshafeey N, Mamindla P, Zinn PO, Ng C, Vikram R, Bakas S, Peterson CB, Rodon Ahnert J, Subbiah V, Karp DD, Stephen B, Hajjar J, Naing A.

Institution: Department of Radiology, University of Pittsburgh, Pittsburgh, PA, USA.

Abstract: The study included 57 patients with advanced rare cancers who were enrolled in our phase II clinical trial of pembrolizumab. Tumor response was evaluated using Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 and immune-related RECIST (irRECIST). Patients were categorized as 20 "controlled disease" (stable disease, partial response, or complete response) or 37 progressive disease). We used 3D Slicer to segment target lesions on standard-of-care, pretreatment contrast enhanced CT scans. We extracted 610 features (10 histogram-based features and 600 second-order texture features) from each volume of interest. Least absolute shrinkage and selection operator logistic regression was used to detect the most discriminatory features. Selected features were used to create a classification model, using XGBoost, for the prediction of tumor response to pembrolizumab. Leave-one-out cross-validation was performed to assess model performance.

Three-Dimensional Evaluation of Maxillary Second Molar Position in Untreated Patients With Normal Occlusion: Implications for Preadjusted Appliance Prescriptions

Publication: J Orofac Orthop. 2021 Mar 30. PMID: 33783560

Authors: Goracci C, Ruellas AC, Nieri M, Crouch S, McNamara JA Jr, Franchi L.

Institution: Department of Medical Biotechnologies, University of Siena, Policlinico Le Scotte, Siena, Italy.

Abstract: A sample of 41 subjects (16 females, 25 males) was selected from the University of Michigan Growth Study (UMGS). Digital dental casts with fully erupted second molars in occlusion were chosen (mean age 14.9 ± 1.3 years). Digital measurements were recorded with the open source software 3D Slicer. The digital measurements of the UMGS sample were compared with the manual measurements collected by Andrews from his sample of untreated class I subjects with normal overbite and overjet. Two mixed effect models (sagittal and transversal inclinations) were performed. The "random effect" was represented by the subjects, while the "fixed effects" were the two compared groups, the side of the arch (right and left), and the group × side interaction. Outcome variables were sagittal and transversal inclinations of the upper second molars.

3D Printing of Rapid, Low-Cost and Patient-Specific Models of Brain Vasculature for Use in Preoperative Planning in Clipping of Intracranial Aneurysms

Publication: J Clin Med. 2021 Mar 13;10(6):1201. PMID: 33805774 | PDF

Authors: Błaszczyk M, Jabbar R, Szmyd B, Radek M.

Institution: Department of Neurosurgery, Spine and Peripheral Nerves Surgery, Medical University of Łódź, Łódź, Poland.

Abstract: We developed a practical and cost-effective method of production of a 3D-printed model of the arterial Circle of Willis of patients treated because of an intracranial aneurysm. We present and explain the steps necessary to produce a 3D model from medical image data, and express the significant value such models have in patient-specific pre-operative planning as well as education. A Digital Imaging and Communications in Medicine (DICOM) viewer is used to create 3D visualization from a patient's Computed Tomography Angiography (CTA) images. After generating the reconstruction, we manually remove the anatomical components that we wish to exclude from the print by utilizing tools provided with the imaging software. We then export this 3D reconstructions file into a Standard Triangulation Language (STL) file which is then run through a 3D Slicer software to generate a G-code file for the printer.


Early Prediction of Putamen Imaging Features in HIV-Associated Neurocognitive Impairment Syndrome

Publication: BMC Neurol. 2021 Mar 9;21(1):106. PMID: 33750319 | PDF

Authors: Qi Y, Xu M, Wang W, Wang YY, Liu JJ, Ren HX, Liu MM, Li RL, Li HJ.

Institution: Department of Radiology, Beijing Youan Hospital, Capital Medical University, Beijing, China.

Abstract: Retrospective selection of 90 patients with HIV infection, including 36 asymptomatic neurocognitive impairment (ANI) patients and 54 pre-clinical ANI patients in Beijing YouAn Hospital. All patients received comprehensive neuropsychological assessment and MRI scanning. 3D Slicer software was used to acquire volume of interest (VOI) and radiomics features.

Use of Volumetric CT Scanning to Predict Tumor Staging and Survival in Pancreatic Cancer Patients That Are to Be Administered Curative Resection

Publication: J Surg Oncol. 2021 May;123(8):1757-63. PMID: 33684252

Authors: Sengul Samanci N, Çelik E, Bagcilar O, Tutar O, Samanci C, Velidedeoglu M, Yassa AE, Demirci NS, Demirelli FH.

Institution: Department of Medical Oncology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey.

Abstract: Methods: Tumor volume was measured from contrast enhanced CT images of 58 patients who undergo curative resection for pancreatic cancer using the Segment Editor module implemented in 3D Slicer, a free open source software platform. Receiver operating characteristic (ROC) analysis was used to evaluate correlation between Tvol and pTNM staging.

Fitting Unbranching Skeletal Structures to Objects

Publication: Med Image Anal. 2021 May;70:102020. PMID: 33743355

Authors: Liu Z, Hong J, Vicory J, Damon JN, Pizer SM.

Institution: Department of Computer Science, University of North Carolina at Chapel Hill, USA.

Abstract: Representing an object by a skeletal structure can be powerful for statistical shape analysis if there is good correspondence of the representations within a population. Many anatomic objects have a genus-zero boundary and can be represented by a smooth unbranching skeletal structure that can be discretely approximated. We describe how to compute such a discrete skeletal structure ("d-s-rep") for an individual 3D shape with the desired correspondence across cases. The method involves fitting a d-s-rep to an input representation of an object's boundary. A good fit is taken to be one whose skeletally implied boundary well approximates the target surface in terms of low order geometric boundary properties: (1) positions, (2) tangent fields, (3) various curvatures. Our method involves a two-stage framework that first, roughly yet consistently fits a skeletal structure to each object and second, refines the skeletal structure such that the shape of the implied boundary well approximates that of the object. The first stage uses a stratified diffeomorphism to produce topologically non-self-overlapping, smooth and unbranching skeletal structures for each object of a population. The second stage uses loss terms that measure geometric disagreement between the skeletally implied boundary and the target boundary and avoid self-overlaps in the boundary. By minimizing the total loss, we end up with a good d-s-rep for each individual shape. We demonstrate such d-s-reps for various human brain structures. The framework is accessible and extensible by clinical users, researchers and developers as an extension of SlicerSALT, which is based on 3D Slicer.

Three-Dimensional Modeling and Automatic Analysis of the Human Nasal Cavity and Paranasal Sinuses Using the Computational Fluid Dynamics Method

Publication: Eur Arch Otorhinolaryngol. 2021 May;278(5):1443-53. PMID: 33068172 | PDF

Authors: Tretiakow D, Tesch K, Meyer-Szary J, Markiet K, Skorek A.

Institution: Department of Otolaryngology, Gdansk Medical University, Gdansk, Poland.

Abstract: This study is based on CT images of 16 patients. Image processing and model generation of the human nasal cavity and paranasal sinuses were performed using open-source and freeware software. 3D Slicer was used primarily for segmentation and new surface model generation. Further processing was done using Autodesk® Meshmixer TM. The governing equations are discretized by means of the finite volume method. Subsequently, the corresponding algebraic equation systems were solved by OpenFOAM software.

Comparison Between Computed Tomography and Silicone-Casting Methods to Determine Gunshot Cavities in Ballistic Soap

Publication: Int J Legal Med. 2021 May;135(3):829-36. PMID: 33190163

Authors: Burgos-Díez I, Zapata F, Chamorro-Sancho MJ, Ruano-Rando MJ, Ferrando-Gil JL, García-Ruiz C, Montalvo G, Ortega-Ojeda F.

Institution: Ballistics and Tool marks Department, Criminalistics Service, Guardia Civil HQ, Madrid, Spain.

Abstract: Current methods used in terminal ballistics to determine the volume of temporary cavities created by projectiles in soft tissue simulants (such as ballistic soap) usually involve silicone-casting to obtain the cavity moulds. However, these methods have important drawbacks including their little sensitivity and precision, besides the fact that they are destructive. Imaging techniques such as computed tomography (CT) might not only overcome those limitations but also offer useful tools for digitally reporting the scientific results. This work accomplished the 3D digital reconstruction of the cavities created by different projectiles in ballistic soap blocks. This way, the total volume of the cavities, the projectile penetration depths, and other measurements were determined, rendering better capabilities when compared to the current silicone method. All these features were achieved through the CT analysis and 3D Slicer imaging software. In addition, it is worth mentioning that the method can preserve the evidence by digitally obtaining, signing, and storing the infographic videos displaying the 3D-reconstructed cavities. Graphical abstract.

A Machine Learning-Based Radiomics Model for the Prediction of Axillary Lymph-Node Metastasis in Breast Cancer

Publication: Breast Cancer. 2021 May;28(3):664-71. PMID: 33454875

Authors: Song BI.

Institution: Department of Nuclear Medicine, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Republic of Korea.

Abstract: A total of 100 consecutive IDC patients who underwent surgical resection of primary tumor with sentinel lymph-node biopsy and/or ALN dissection without any neoadjuvant treatment were analyzed. Volume of interests (VOIs) were drawn more than 2.5 of standardized uptake value in the primary tumor on the PET scan using 3D Slicer. Pyradiomics package was used for the extraction of texture features in python. The radiomics prediction model for ALN metastasis was developed in 75 patients of the training cohort and validated in 25 patients of the test cohort. XGBoost algorithm was utilized to select features and build radiomics model. The sensitivity, specificity, and accuracy of the predictive model were calculated.

Cost-Effective Fetal Lung Volumetry for Assessment of Congenital Diaphragmatic Hernia

Publication: Eur J Obstet Gynecol Reprod Biol. 2021 May;260:22-8. PMID: 33713885

Authors: Corroenne R, Zhu KH, Johnson R, Mehollin-Ray AR, Shamshirsaz AA, Nassr AA, Belfort MA, Cortes MS, Shetty A, Lee W, Espinoza J.

Institution: Department of Obstetrics and Gynecology, Texas Children's Hospital & Baylor College of Medicine, Houston, TX, USA.

Abstract: Objectives: (1) To investigate the reproducibility of total fetal lung volume (TFLV) measurements using a free 3D modeling software, 3D Slicer; (2) To correlate these measurements with lung-to-head ratio (LHR) or TFLV measured using PACS and; (3) To determine the role of 3DSlicer in predicting perinatal outcomes in cases with congenital diaphragmatic hernia (CDH) who had fetal tracheal occlusion (FETO).

The Role of Recipient Myosteatosis in Graft and Patient Survival After Deceased Donor Liver Transplantation

Publication: J Cachexia Sarcopenia Muscle. 2021 Apr;12(2):358-67. PMID: 33525056 | PDF

Authors: Czigany Z, Kramp W, Lurje I, Miller H, Bednarsch J, Lang SA, Ulmer TF, Bruners P, Strnad P, Trautwein C, von Websky MW, Tacke F, Neumann UP, Lurje G.

Institution: Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany. 

Abstract: Clinical data from 225 consecutive OLT recipients from a prospective database were retrospectively analysed (May 2010 to December 2017). Computed tomography‐based lumbar skeletal muscle index (SMI) (muscle mass) and mean skeletal muscle radiation attenuation (SM‐RA) (myosteatosis) were calculated using a segmentation tool, 3D Slicer. Patients with low skeletal muscle mass (low SMI) and myosteatosis (low SM‐RA) were identified using predefined and validated cut‐off values.

3D-Assisted Mandibular Reconstruction: A Technical Note of Fibula Free Flap With Preshaped Titanium Plate

Publication: Ann Chir Plast Esthet. 2021 Apr;66(2):174-9. PMID: 32753249

Authors: Villa S, Druelle C, Juliéron M, Nicot R.

Institution: Service de chirurgie maxillo-faciale et stomatologie, university de Lille, Lille cedex, France.

Abstract: The purpose of this technical note is to illustrate a simple and economical preoperative method for preshaping a reconstructive titanium plate in a fibula free flap (FFF) by using 3D printing of a virtually reconstructed mandible haptic model. The whole process consisted in creating a 3D model of the patient's mandible based on a CT-scan using a combination of free software (3D Slicer and ITK-snap), and simulating the surgical osteotomies and reconstruction, and print it as a guide for bending a reconstruction titanium plate. Reconstruction is performed using virtual cubes (1 to 3 cubes, according the number of FFF osteotomies). This virtual lab work is performed using 3D Builder® (Microsoft, Redmond) software. This technique allows obtaining an optimal plate application on the bony fragments. It facilitates reconstructive surgery with good functional (putting the patient back in an optimal dental occlusion based on the native maxilla) and aesthetic results. This technical note presents a simple and economical preoperative fabrication of a reconstructive plate through freeware and a low-cost 3D printer accessible to all surgeons.

Radiomics Approaches for Predicting Liver Fibrosis With Nonenhanced T1 -Weighted Imaging: Comparison of Different Radiomics Models

Publication: J Magn Reson Imaging. 2021 Apr;53(4):1080-9. PMID: 33043991

Authors: Ni M, Wang L, Yu H, Wen X, Yang Y, Liu G, Hu Y, Li Z.

Institution: Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China.

Abstract: Liver fibrosis rats were induced via subcutaneous injection of a mixture of carbon tetrachloride. Rats in the control group were injected with saline. Segmentation and feature extraction were performed by 3D Slicer and the image biomarker explorer (IBEX) software package. Data preprocessing, feature selection, model building, and model comparative evaluation were conducted with Python. The liver fibrosis stage was determined by pathological examination.

Clinical 3D Imaging of the Anterior Segment With Ultrasound Biomicroscopy

Publication: Transl Vis Sci Technol. 2021 Mar 1;10(3):11. PMID: 34003945 | PDF

Authors: Helms RW, Minhaz AT, Wilson DL, Örge FH.

Institution: Center for Pediatric Ophthalmology and Adult Strabismus, Rainbow Babies and Children's Hospital, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.

Abstract: Ultrasound biomicroscopy (UBM) is an important ophthalmic imaging modality due to its ability to see behind pigmented iris and to visualize anterior chamber when the eye's transparency is compromised. We created a three-dimensional UBM (3D-UBM) system and acquired example images to illustrate its potential.

In vivo imaging of rabbit anterior chamber. Rabbits were sedated, and the probe was attached to a flexible arm and positioned over the rabbit's eye. The AC was scanned using 100 frames. The AC was manually segmented (3D Slicer software) to determine AC volume and depth. This figure shows the segmented AC (green) with part of the cornea cropped away.

Prognosis Predicting Value of Semiquantitative Parameters of Visceral Adipose Tissue and Subcutaneous Adipose Tissue of 18F-FDG PET/CT in Newly Diagnosed Secondary Hemophagocytic Lymphohistiocytosis

Publication: Ann Nucl Med. 2021 Mar;35(3):386-96. PMID: 33469854

Authors: Liu J, Yang X, Yang J.

Institution: Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.

Abstract: We retrospectively collected 58 patients with newly diagnosed SHLH from August 2016 to July 2019 in our hospital. All patients were followed up between 6 and 24 months. First, a comprehensive comparison of the general data between the death and the survival group was performed. Clinical lab indexes included were recorded and analyzed retrospectively. Second, the correlation between 18F-FDG PET/CT semiquantitative metabolic parameters of VAT, SAT and inflammatory cytokines was performed. 3D Slicer software was used to get SUV and volume of VAT and SAT from 18F-FDG PET/CT. Third, overall survival (OS) analysis was performed. Finally, the prognosis predicting model was built based on risk factors to stratify SHLH patients.

An Open-Source Three-Dimensionally Printed Laryngeal Model for Injection Laryngoplasty Training

Publication: Laryngoscope. 2021 Mar;131(3):E890-E895. PMID: 32750164

Authors: Lee M, Ang C, Andreadis K, Shin J, Rameau A.

Institution: Sean Parker Institute for the Voice, Department of Otolaryngology-Head and Neck Surgery, Weill Cornell Medicine, New York, NY, USA.

Abstract: Computed tomography scans of the upper airways were processed with 3D Slicerto generate a computer model of the endolarynx. Blender and Fusion 360 were used to refine the mucosal model and develop casts for silicone injection molding. The casted endolaryngeal structures were inserted into a modified version of a publicly available laryngeal cartilage model. The final models were evaluated by 10 expert laryngologists using a customized version of the Michigan Standard Simulation Experience Scale. Internal consistency and interrater reliability of the survey were evaluated using Cronbach's α and intraclass correlation, respectively.

Treatment Measures of Hemimandibular Hyperplasia and Associated Facial Deformities

Publication: J Craniomaxillofac Surg. 2021 Feb;49(2):126-34. PMID: 33451941

Authors: Abotaleb B, Bi R, Telha W, Zhao W, Li Y, Zhu S.

Institution: State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.

Abstract: This study aims to show our institute's experience in the treatment of HH and its associated facial deformities in adults and growing adolescents and to investigate condylar remodeling and volumetric changes and long-term stability of orthognathic surgery in adults. The study included consecutive patients with clinical and radiological features of HH who underwent high condylectomy with or without simultaneous orthognathic surgery from 2013 to 2018. The clinical outcomes were assessed based on functional activities, TMJ pain, and recurrence. Postoperative 3D condylar remodeling and orthognathic stability were evaluated with the use of ITK-Snap and 3D Slicer. Thirteen patients (8 females and 5 males) with a mean age of 26.3 ± 5.79 years (range; 13-34 years) were included with facial asymmetry as the chief complaint. The patients were followed up for a minimum of 12 months and a maximum of 4 years (mean; 16.85 ± 10.04). There were no postoperative complications, and all patients achieved a satisfactory functional and aesthetic outcome using a one-stage surgical procedure. There was no incidence of recurrence or further asymmetries, with long-term stability at the selected points showing a mean difference of less than ±1 mm. The affected condylar volume was significantly reduced following high condylectomy, with mean changes between T1 and T2 of -144. 80 mm3 (p = .012). However, the contralateral condylar volume remained stable, with a mean change of 2.54 mm3 (p = .881). One-stage high condylectomy and orthognathic surgery is a viable measure for the treatment of HH and associated deformities in adults. High condylectomy in early adolescence could result in termination of the disease, and aesthetic improvement with further constant orthodontist-surgeon follow-up is required.

Three-Dimensional Evaluation of Dental Decompensation and Mandibular Symphysis Remodeling on Orthodontic-Surgical Treatment of Class III Malocclusion

Publication: Am J Orthod Dentofacial Orthop. 2021 Feb;159(2):184-92. PMID: 33388202 | PDF

Authors: Sendyk M, Cevidanes LHS, Ruellas ACO, Fattori L, Mendes FM, Paiva JB, Rino Neto J.

Institution: Department of Orthodontics, School of Dentistry, University of São Paulo, São Paulo, Brazil.

Abstract: The sample consisted of 30 adults with Class III dentofacial deformity, who had presurgical orthodontic treatment. Three-dimensional images were generated by cone-beam computed tomography scans at 2 different times (initial and before orthognathic surgery). Three-dimensional virtual models were obtained and superimposed using automated voxel-based registration at the mandible to evaluate B-point displacement, mandibular molar and incisor decompensation movement, and symphysis inclination and thickness. The 3-dimensional displacements of landmarks at the symphysis were quantified and visualized with color-coded maps using 3D Slicer v.4.0. software.

A CT-Based Radiomics Nomogram for Distinguishing Between Benign and Malignant Bone Tumours

Publication: Cancer Imaging. 2021 Feb 6;21(1):20. PMID: 33549151 PDF

Authors: Sun W, Liu S, Guo J, Liu S, Hao D, Hou F, Wang H, Xu W.

Institution: Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.

Abstract: Background: We sought to evaluate the performance of a computed tomography (CT)-based radiomics nomogram we devised in distinguishing benign from malignant bone tumours.

Methods: Two hundred and six patients with bone tumours were spilt into two groups: a training set (n = 155) and a validation set (n = 51). A feature extraction process based on 3D Slicer software was used to extract the radiomics features from unenhanced CT images, and least absolute shrinkage and selection operator logistic regression was used to calculate the radiomic score to generate a radiomics signature. A clinical model comprised demographics and CT features. A radiomics nomogram combined with the clinical model and the radiomics signature was constructed. The performance of the three models was comprehensively evaluated from three aspects: identification ability, accuracy, and clinical value, allowing for generation of an optimal prediction model.

A Supplemental Technique for Preoperative Evaluation of Giant Intracranial Aneurysm

Publication: J Neurol Surg A Cent Eur Neurosurg. 2021 Feb 14. PMID: 33583010

Authors: Wang HW, Wu C, Xue Z, Shu XJ, Sun ZH.

Institution: Chinese PLA General Hospital, Neurosurgery, Beijing, China.

Abstract: Preoperative planning mainly relies on digital subtraction angiography (DSA) and computed tomography angiography. However, neither technique can reveal thrombi in giant intracranial aneurysms (GIAs). In this study, we aimed to reconstruct the circulating and noncirculating parts of GIAs with the time-of-flight (TOF) and motion-sensitized driven-equilibrium (MSDE) sequences with 3D Slicer to reveal an integrated presentation of GIAs, compare its accuracy, and validate the usefulness for preoperative planning.

Maxillary Dentoskeletal Outcomes of the Expander With Differential Opening and the Fan-Type Expander: A Randomized Controlled trialA Supplemental Technique for Preoperative Evaluation of Giant Intracranial Aneurysm

Publication: Clin Oral Investig. 2021 Feb 12. PMID: 33580351

Authors: Massaro C, Garib D, Cevidanes L, Janson G, Yatabe M, Lauris JRP, Ruellas AC.

Institution: Department of Orthodontics, Bauru Dental School, University of São Paulo, Brazil.

Abstract: The aim of this study was to compare the maxillary dentoskeletal outcomes of the expander with differential opening (EDO) and the fan-type expander (FE).

Material and methods: Forty-eight patients with maxillary arch constriction in the mixed dentition were randomly allocated into EDO and FE groups. Cone-beam computed tomography scans were acquired before and after expansion. Linear and angular three-dimensional changes were assessed after cranial base superimposition using the ITK-SNAP and the 3D Slicer software. T or Mann-Whitney U tests were used for intergroup comparisons (P<0.05).

Positron Emission Tomography-Based Short-Term Efficacy Evaluation and Prediction in Patients With Non-Small Cell Lung Cancer Treated With Hypo-Fractionated Radiotherapy

Publication: Front Oncol. 2021 Feb 25;11:590836. PMID: 33718144 | PDF

Authors: Jiang YQ, Gao Q, Chen H, Shi XX, Wu JB, Chen Y, Zhang Y, Pang HW, Lin S.

Institution: Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.

Abstract: The 3D Slicer was used to extract the radiomics features based on positron emission tomography. Least absolute shrinkage and selection operator regression was used to eliminate redundant features, and logistic regression analysis was used to develop the curative-effect-predicting model, which was displayed through a radiomics nomogram. Receiver operating characteristic curve and decision curve were used to evaluate the accuracy and clinical usefulness of the prediction model.

Radiomics-Based Machine Learning Model to Predict Risk of Death Within 5-Years in Clear Cell Renal Cell Carcinoma Patients

Publication: Comput Biol Med. 2021 Feb;129:104135. PMID: 33254045

Authors: Nazari M, Shiri I, Zaidi H.

Institution: Department of Biomedical Engineering and Medical Physics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Abstract: According to image quality and clinical data availability, we eventually selected 70 ccRCC patients that underwent CT scans. Manual volume-of-interest (VOI) segmentation of each image was performed by an experienced radiologist using the 3D Slicer software package. Prior to feature extraction, image pre-processing was performed on CT images to extract different image features, including wavelet, Laplacian of Gaussian, and resampling of the intensity values to 32, 64 and 128 bin levels. Overall, 2544 3D radiomics features were extracted from each VOI for each patient. Minimum Redundancy Maximum Relevance (MRMR) algorithm was used as feature selector. Four classification algorithms were used, including Generalized Linear Model (GLM), Support Vector Machine (SVM), K-nearest Neighbor (KNN) and XGBoost. We used the Bootstrap resampling method to create validation sets. Area under the receiver operating characteristic (ROC) curve (AUROC), accuracy, sensitivity, and specificity were used to assess the performance of the classification models.

Exploring the Variability of Radiomic Features of Lung Cancer Lesions on Unenhanced and Contrast-Enhanced Chest CT Imaging

Publication: Phys Med. 2021 Feb;82:321-31. PMID: 33721791

Authors: Tamponi M, Crivelli P, Montella R, Sanna F, Gabriele D, Poggiu A, Sanna E, Marini P, Meloni GB, Sverzellati N, Conti M.

Institution: Health Physics Unit, ATS Sardinia Regional Health Service, Sassari, Italy.

Abstract: Chest CT scans, unenhanced and contrast-enhanced, of 17 patients were selected from images collected as part of the staging process. The major T1-T3 lesion was contoured through a semi-automatic approach. These lesions formed the lesion phantoms to study features behavior. The stability of 94 features of the 3D Slicerr package Radiomics was analyzed. Feature discrimination power was quantified by means of Gini's coefficient. Correlation between distance matrices was evaluated through Mantel statistic. Heatmap, cluster and silhouette plots were applied to find well-structured partitions of lesions.

Regenerative Orthodontics: GBR and Corticotomy to Stretch the Limits of Orthodontic Treatment

Publication: Int J Periodontics Restorative Dent. 2021 Jan-Feb;41(1):105-11. PMID: 33528458

Authors: Brugnami F, Caiazzo A, Signorelli L, Capri D.


Abstract: Orthodontic therapy could lead to marginal bone resorption in cases where the teeth are moved outside the envelope of bone. The purpose of this case series was to test corticotomy with a guided bone regeneration (GBR) procedure to regenerate bone in the direction of movement outside the original bony housing. Ten adult patients (60 anterior teeth), all presenting with severe anterior crowding, were enrolled in the study. Orthodontic therapy in all investigated sites was associated with selective surgical corticotomies and a simultaneous GBR procedure. CBCT examinations were performed before starting orthodontic treatment (T0) and at the end of treatment (T1; mean: 7 months; range: 6 to 9 months). Pre- and postoperative CBCTs were superimposed with a DICOM viewer 3D Slicer and studied with an image-processing software (ImageJ, National Institutes of Health) to measure the area of interest of the buccal plate. The average area was found to be 0.58 ± 0.22 mm2 at T0 and 1.76 ± 0.4 mm2 at T1, with a statistically significant difference (P < .05). The combination of corticotomy and a regenerative procedure seems to have the ability to augment the original osseous anatomy when the root is moved outside of the original bony envelope.

The Effects of Age and Race on Calvarium, Tegmen, and Zygoma Thickness

Publication: J Craniofac Surg. 2021 Jan-Feb 01;32(1):345-9. PMID: 32890157

Authors: Saltagi MZ, Schueth E, Nag A, Rabbani C, MacPhail ME, Nelson RF.

Institution: Department of Neurosurgery, Indiana University School of Medicine, Indianapolis, IN, USA.

Abstract: A total of 446 patients with high-resolution head computer tomography (CT) imaging from 2003 to 2018.Intervention(s): Calvarial, tegmen, and zygoma thicknesses were measured using 3D Slicer. Main Outcome Measure(s): Effects of age and race on calvarium, tegmen, zygoma thickness.

Novel Workflow for Conversion of Catheter-Based Electroanatomic Mapping to DICOM Imaging for Noninvasive Radioablation of Ventricular Tachycardia

Publication: Pract Radiat Oncol. 2021 Jan-Feb;11(1):84-8. PMID: 32416269

Authors: Brett CL, Cook JA, Aboud AA, Karim R, Shinohara ET, Stevenson WG.

Institution: Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.

Abstract: The raw data export of the CARTO3 EAM system (version 6.0.45.171, ".mesh" file) was processed with a MATLAB script to generate 3-dimensional (3D) visual took kit files containing X, Y, Z coordinates obtained during mapping and corresponding impedance, voltage, and other point-based information. The image could then be visualized with standard image processing software, 3D Slicer and the target outlined on the image surface. This structure was in turn converted to a DICOM image and fused with patient thoracic imaging using anatomic landmarks. Robustness of the workflow was assessed through implementation with a second magnetic resonance imaging based VT ablation planning system, ADAS-VT.

Deformation of the Pelvic Arteries Caused by Pneumoperitoneum and Postural Changes in an Animal Model

Publication: In Vivo. 2021 Jan-Feb;35(1):275-81. PMID: 33402474 | PDF

Authors: Kiyomatsu H, Ma L, Wang J, Kiyomatsu T, Tsukihara H, Kobayashi E, Sakuma I, Ishihara S.

Institution: Department of Surgical Oncology, Faculty of Medicine, The University of Tokyo, Tokyo, Japan.

Abstract: Computed tomography images of pigs were acquired in different body positions (supine, head down at 5° and 10°, right lateral recumbent at 5° and 15°) before and after insufflation. We used a free software, 3D Slicer, for image analysis. After landmark registration using 10 markers inserted into the pelvis, pelvic arterial deformation and shift of seven arterial bifurcation points were evaluated. The distance moved was the target registration error (TRE) from the points registered in the supine position. Fiducial registration error (FRE) was measured using the 10 pelvic markers.

Development and Validation of a CT-Based Nomogram for Preoperative Prediction of Clear Cell Renal Cell Carcinoma Grades

Publication: Eur Radiol. 2021 Jan 29. PMID: 33515086

Authors: Zheng Z, Chen Z, Xie Y, Zhong Q, Xie W.

Institution: Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.

Abstract: CT images and clinical data of 258 ccRCC patients were retrieved from the Cancer Imaging Archive (TCIA). Radiomics features were extracted from arterial-phase CT images using 3D Slicer software.

CardIAc: An Open-Source Application for Myocardial Strain Analysis

Publication: Int J Comput Assist Radiol Surg. 2021 Jan;16(1):65-79. PMID: 33196972

Authors: Curiale AH, Bernardo A, Cárdenas R, Mato G.

Institution: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.

Abstract: CardIAc was developed as a 3D Slicer extension for an easy installation and usability. The main contribution of this article is to provide a general workflow, going from data and segmentation loading, 3D heart modeling, analysis and several options for visualization of the myocardial strain.

Endoscope-Assisted Fluorescence-Guided Resection Allowing Supratotal Removal in Glioblastoma Surgery

Publication: Neurosurg Focus. 2021 Jan;50(1):E3. PMID: 33386004

Authors: Bettag C, Schregel K, Langer P, Thomas C, Behme D, Stadelmann C, Rohde V, Mielke D.

Institution: Department of Neuroradiology, University Hospital Heidelberg, Germany.

Abstract: The authors conducted a retrospective single-center analysis of a consecutive series of patients with primary GBM presumed to be noneloquently located and routinely operated on at their institution between January 2015 and February 2018 using a combined microscopic and endoscopic FG resection. A 20-mg/kg dose of 5-aminolevulinic acid (5-ALA) was administered 4 hours before surgery. After complete microscopic FG resection, the resection cavity was scanned using the endoscope. Detected residual fluorescent tissue was resected and embedded separately for histopathological examination. Nonenhanced and contrast-enhanced 3D T1-weighted MR images acquired before and within 48 hours after tumor resection were analyzed using 3D Slicer. Bias field-corrected data were used to segment brain parenchyma, contrast-enhancing tumor, and the resection cavity for volume definition. The difference between the pre- and postoperative brain parenchyma volume was considered to be equivalent to the resected nonenhancing but fluorescent tumor tissue. The volume of resected tumor tissue was calculated from the sum of resected contrast-enhancing tumor tissue and resected nonenhancing tumor tissue.

Clinical and Radiological Predictors of Epidermal Growth Factor Receptor Mutation in Nonsmall Cell Lung Cancer

Publication: J Appl Clin Med Phys. 2021 Jan;22(1):271-80. PMID: 33314737 | PDF

Authors: Dang Y, Wang R, Qian K, Lu J, Zhang H, Zhang Y.

Institution: Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China.

Abstract: Patients with NSCLC who underwent EGFR mutation detection between 2014 and 2017 were included. Clinical features and general imaging features were collected, and radiomic features were extracted from CT data by 3D Slicer software. Prognostic factors of EGFR mutation status were selected by least absolute shrinkage and selection operator (LASSO) logistic regression analysis, and receiver operating characteristic (ROC) curves were drawn for each prediction model of EGFR mutation.

A User-Friendly Protocol for Mandibular Segmentation of CBCT Images for Superimposition and Internal Structure Analysis

Publication: J Clin Med. 2021 Jan 1;10(1):127. PMID: 33401443 | PDF

Authors: Li C, Lin L, Zheng Z, Chung CH.

Institution: Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Abstract: The "sculpting tool" in the Dolphin 3D Imaging software was used for segmentation. The segmented mandible images were saved as STL files for volume matching in the 3D Slicer to validate the repeatability of the current protocol and were exported as DICOM files for internal structure analysis and voxel-based superimposition.

Development, Validation, and Pilot MRI Safety Study of a High-Resolution, Open Source, Whole Body Pediatric Numerical Simulation Model

Publication: PLoS One. 2021 Jan 13;16(1):e0241682. PMID: 33439896 | PDF

Authors: Jeong H, Ntolkeras G, Alhilani M, Atefi SR, Zöllei L, Fujimoto K, Pourvaziri A, Lev MH, Grant PE, Bonmassar G.

Institution: Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.

Abstract: Numerical body models of children are used for designing medical devices, including but not limited to optical imaging, ultrasound, CT, EEG/MEG, and MRI. These models are used in many clinical and neuroscience research applications, such as radiation safety dosimetric studies and source localization. Although several such adult models have been reported, there are few reports of full-body pediatric models, and those described have several limitations. Some, for example, are either morphed from older children or do not have detailed segmentations. Here, we introduce a 29-month-old male whole-body native numerical model, "MARTIN", that includes 28 head and 86 body tissue compartments, segmented directly from the high spatial resolution MRI and CT images. An advanced auto-segmentation tool was used for the deep-brain structures, whereas 3D Slicer was used to segment the non-brain structures and to refine the segmentation for all of the tissue compartments. Our MARTIN model was developed and validated using three separate approaches, through an iterative process, as follows. First, the calculated volumes, weights, and dimensions of selected structures were adjusted and confirmed to be within 6% of the literature values for the 2-3-year-old age-range. Second, all structural segmentations were adjusted and confirmed by two experienced, sub-specialty certified neuro-radiologists, also through an interactive process. Third, an additional validation was performed with a Bloch simulator to create synthetic MR image from our MARTIN model and compare the image contrast of the resulting synthetic image with that of the original MRI data; this resulted in a "structural resemblance" index of 0.97. Finally, we used our model to perform pilot MRI safety simulations of an Active Implantable Medical Device (AIMD) using a commercially available software platform (Sim4Life), incorporating the latest International Standards Organization guidelines. This model will be made available on the Athinoula A. Martinos Center for Biomedical Imaging website.

Condylar Changes in Children with Posterior Crossbite after Maxillary Expansion: Tridimensional Evaluation

Publication: Children (Basel). 2021 Jan 11;8(1):38. PMID: 33440762 | PDF

Authors: Fastuca R, Turiaco H, Assandri F, Zecca PA, Levrini L, Caprioglio A.

Institution: Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy.

Abstract: To investigate condylar position in subjects with functional posterior crossbite comparing findings before and after rapid maxillary expansion (RME) treatment through 3D analysis. Methods: Thirty-two Caucasian patients (14 males, mean age 8 y 8 m ± 1 y 2 m; 18 females mean age 8 y 2 m ± 1 y 4 m) with functional posterior crossbite (FPXB) diagnosis underwent rapid palatal expansion with a Haas appliance banded on second deciduous upper molars. Patients' underwent CBCT scans before rapid palatal expansion (T0) and after 12 months (T1). The images were processed through 3D Slicer software; Results: The condylar position changes between T1 and T0 among the crossbite and non-crossbite sides were not statistically significant, except for the transversal axis. At T1, the condyles moved forward (y axis) and laterally (x axis), they also moved downward (z axis) but not significantly; (4) Conclusions: Condilar position in growing patients with functional posterior crossbite did not change significantly after rapid maxillary expansion.

New Insights Into Intrinsic Foot Muscle Morphology and Composition Using Ultra-High-Field (7-Tesla) Magnetic Resonance Imaging

Publication: BMC Musculoskelet Disord. 2021 Jan 21;22(1):97. PMID: 33478467 | PDF

Authors: Franettovich Smith MM, Elliott JM, Al-Najjar A, Weber KA 2nd, Hoggarth MA, Vicenzino B, Hodges PW, Collins NJ.

Institution: School of Health and Rehabilitation Sciences, The University of Queensland, QLD, Australia

Abstract: One healthy female (age 39 years, mass 65 kg, height 1.73 m) underwent MRI. A T1-weighted VIBE - radio-frequency spoiled 3D steady state GRE - sequence of the whole foot was acquired on a Siemens 7T MAGNETOM scanner, as well as a 3T MAGNETOM Prisma scanner for comparison. A high-resolution fat/water separation image was also acquired using a 3D 2-point DIXON sequence at 7T. Coronal plane images from 3T and 7T scanners were compared. Using 3D Slicer software, regions of interest were manually contoured for each muscle on 7T images. Muscle volumes and percentage of muscle fat infiltration were calculated (muscle fat infiltration % = Fat/(Fat + Water) x100) for each muscle.

3D-Volume Rendering of the Pelvis With Emphasis on Paraurethral Structures Based on MRI Scans and Comparisons Between 3D Slicer and OsiriX®

Publication: AJ Med Syst. 2021 Jan 20;45(3):27. PMID: 33469726 | PDF

Authors: Durnea CM, Siddiqi S, Nazarian D, Munneke G, Sedgwick PM, Doumouchtsis SK.

Institution: Epsom & St. Helier University Hospitals NHS Trust, Epsom, UK.

Abstract: The feasibility of rendering three dimensional (3D) pelvic models of vaginal, urethral and paraurethral lesions from 2D MRI has been demonstrated previously. To quantitatively compare 3D models using two different image processing applications: 3D Slicer and OsiriX. Secondary analysis and processing of five MRI scan based image sets from female patients aged 29–43 years old with vaginal or paraurethral lesions. Cross sectional image sets were used to create 3D models of the pelvic structures with 3D Slicer and OsiriX image processing applications. The linear dimensions of the models created using the two different methods were compared using Bland-Altman plots. The comparisons demonstrated good agreement between measurements from the two applications. The two data sets obtained from different image processing methods demonstrated good agreement. Both 3D Slicer and OsiriX can be used interchangeably and produce almost similar results. The clinical role of this investigation modality remains to be further evaluated.

Shape of the Cochlear Basal Turn: An Indicator for an Optimal Electrode-to-Modiolus Proximity With Precurved Electrode Type

Publication: Ear Nose Throat J. 2021 Jan;100(1):38-43. PMID: 32330070 | PDF

Authors: Khurayzi T, Dhanasingh A, Almuhawas F, Alsanosi A.

Institution:King Abdullah Ear Specialist Center, 37850King Saud University, Riyadh, Saudi Arabia.

Abstract: Computed tomography (CT) preoperative image-data sets of 117 ears were made available for the measurements of cochlear parameters retrospectively. 3D Slicer was used in the visualization and measurement of cochlear parameters from both 3D and 2D (2-dimensional) images of the inner ear. Cochlear parameters including basal turn diameter (A), width of the basal turn (B), and cochlear height (H) were measured from the appropriate planes. B/A ratio was made to investigate which ratios correspond to round and elliptical shape of the cochlear basal turn.

The Use of Magnetic Resonance Imaging Technique and 3D Printing in Order to Develop a Three-Dimensional Fistula Model for Patients With Crohn's Disease: Personalised Medicine

Publication: Prz Gastroenterol. 2021;16(1):83-88. PMID: 33986892

Authors: Guz W, Ożóg Ł, Aebisher D, Filip R.

Institution: Department of Electroradiology, Medical College of Rzeszów University, University of Rzeszow, Rzeszow, Poland.

Abstract: MRI at 1.5T and a 3D printer were used. DICOM (Digital imaging and communications in medicine) images were imported into 3D Slicer v.4.8.0. Firstly, anal fistula was modelled on the basis of axial images. Fistula locations, the anus and anal canal, were marked with different coloured markers.

Impact of 3D Printing in Surgical Planning of Congenital Heart Disease

Publication: Arch Cardiol Mex. 2021;91(1):1-6. PMID: 33661871

Authors: Cano-Zárate R, Hernández-Barajas EK, Hernández-Barajas HH, Meave-González A, Espínola-Zavaleta N.

Institution: Departamento de Cardiología Nuclear, Instituto Nacional de Cardiología Ignacio Chávez. Ciudad de México, México.

Abstract: Congenital heart disease makes up for 30% of all congenital anomalies. The prevalence is 8/1,000 live newborns, without predominance of gender. Imaging methods such as echocardiography, angiography, computed tomography or magnetic resonance imaging must be routinely used in congenital heart disease. The mentioned methods can provide virtual reconstructions in volumetric reconstruction or in three dimensional (3D), but only 3D-printed heart models can provide real 3D tactile replicas of cardiac anatomy.

Objective: To make 3D printed heart models in order to provide real 3D tactile replicas of the cardiac anatomy that allow a detailed visualization from all possible perspectives, either of extracardiac or intracardiac structures.

Methods: This information is useful for surgical decision making, especially in patients with complex cardiac defects. DICOM, edited in a software package 3D Slicer v.4.3 and exported for printing in file format (.stl).

Results and conclusions: With 3D printing, the intracardiac and extracardiac anatomy can be evaluated in detail with real-scale cardiac models of the patient, avoiding unexpected findings. This technique is very useful especially in complex congenital heart defects, since it allows precise planning of the surgical procedure.

Association of White Matter Hyperintensity Progression with Cognitive Decline in Patients with Amnestic Mild Cognitive Impairment

Publication: J Alzheimers Dis. 2021;80(2):877-83. PMID: 33579856 PDF

Authors: Hirao K, Yamashita F, Tsugawa A, Haime R, Fukasawa R, Sato T, Kanetaka H, Umahara T, Sakurai H, Hanyu H, Shimizu S.

Institution: Department of Geriatric Medicine, Tokyo Medical University, Shinjuku-ku, Tokyo, Japan.

Abstract: Background: White matter hyperintensities (WMH) on MRI have been reported to increase the risk of conversion from mild cognitive impairment (MCI) to Alzheimer's disease (AD). However, effects of the progression of WMH on the cognition of patients with MCI remains unclear to date.

Objective: To investigate the association between WMH progression and cognitive decline in amnestic MCI patients.

Methods: Thirty-eight subjects with amnestic MCI were analyzed prospectively every year for 2 years. Fourteen MCI subjects dropped out on the final visit, and therefore 24 subjects with MCI were analyzed for the entire duration. The volumes of periventricular hyperintensities (PVH) and deep WMH (DWMH) were measured on T2 FLAIR using the 3D Slicer. The associations between PVH/DWMH progression and cognitive decline were investigated.

Results: An increase in DWMH volume significantly correlated with changes in Mini-Mental State Examination and category verbal fluency scores, whereas an increase in PVH volume did not correlate with changes in any item.

Conclusion: DWMH progression was closely associated with a decline in frontal lobe function and semantic memory, suggesting that WMH progression might affect some AD pathophysiologies in amnestic MCI patients.