Main Page/SlicerCommunity/2021

---

Go to 2022 :: 2021 :: 2020 :: 2019 :: 2018 :: 2017 :: 2016 :: 2015 :: 2014-2011 :: 2010-2000

---

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

• 1,467,466+ downloads in the last 11 years (269,677 in 2023, 206,541 in 2022)
• over 17.900+ literature search results on Google Scholar
  • 13,400+ cancer
  • 7.290+ brain
  • 6,380+ lung
  • 3,980+ breast
  • 3,080+ prostate

• 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.

• 39 events in open source hackathon series continuously running since 2005 with 3260 total participants
• Slicer Forum with +8,138 subscribers has approximately 275 posts every week

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.

2021

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.

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.

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.