Main Page/SlicerCommunity/2021

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The community that relies on 3D Slicer is large and active: (numbers below updated on December 1st, 2023)

  • 2,147+ papers on PubMed citing the Slicer platform paper
    • Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F.M., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network. Magnetic Resonance Imaging. 2012 Nov;30(9):1323-41. PMID: 22770690. PMCID: PMC3466397.


The following is a sample of the research performed using 3D Slicer outside of the group that develops it. in 2021

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

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.

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):191-195. 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.

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.

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: BMC Med Educ. 2021 Apr 6;21(1):194. 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.

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.

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.

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."

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.

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).

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.

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.

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.

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):877-883. 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.

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