The community that relies on 3D Slicer is large and active: (numbers below updated on December 1st, 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
- 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.
- 1 2021
- 1.1 A Multicontrast MR Atlas of the Wistar Rat Brain
- 1.2 Methods for Intratumoral Microdialysis Probe Targeting and Validation in Murine Brain Tumor Models
- 1.3 Testing the Reliability of CT Scan-Based Dental Wear Magnitude Scoring
- 1.4 The Topology of Ventricle Surfaces and Its Application in the Analysis of Hydrocephalic Ventricles: A Proof-of-Concept Study
- 1.5 Prediction of Locoregional Recurrence-Free Survival of Oesophageal Squamous Cell Carcinoma After Chemoradiotherapy Based on an Enhanced CT-Based Radiomics Model
- 1.6 Prediction of the Recurrence of Non-Functioning Pituitary Adenomas Using Preoperative Supra-Intra Sellar Volume and Tumor-Carotid Distance
- 1.7 Analysis of Changes in the Volume of Edema Around Brain Contusions and the Influencing Factors: A Single-Center, Retrospective, Observational Study
- 1.8 Hybrid Additive Fabrication of a Transparent Liver with Biosimilar Haptic Response for Preoperative Planning
- 1.9 The Impact of Tumor Edema on T2-Weighted 3T-MRI Invasive Breast Cancer Histological Characterization: A Pilot Radiomics Study
- 1.10 A Comparative Study Between State-of-the-Art MRI Deidentification and AnonyMI, a New Method Combining Re-Identification Risk Reduction and Geometrical Preservation
- 1.11 Three-Dimensional Structure of the Basal Lamella of the Middle Turbinate
- 1.12 Flatness of the Meckel Cave May Cause Primary Trigeminal Neuralgia: A Radiomics-Based Study
- 1.13 An Unsupervised Learning Approach to Ultrasound Strain Elastography With Spatio-Temporal Consistency
- 1.14 A Mandible with the Temporomandibular Joint-A New FEM Model Dedicated to Strength and Fatigue Calculations of Bonding Elements Used in Fracture and Defect Surgery
- 1.15 Mini Hyrax vs Hyrax Expanders in the Rapid Palatal Expansion in Adolescents With Posterior Crossbite: A Randomized Controlled Clinical Trial
- 1.16 A Novel Dynamic Electromagnetic Tracking Navigation System for Distal Locking of Intramedullary Nails
- 1.17 TorchIO: A Python Library for Efficient Loading, Preprocessing, Augmentation and Patch-Based Sampling of Medical Images in Deep Learning
- 1.18 Virtual Planning and CAD/CAM-Assisted Distraction for Maxillary Hypoplasia in Cleft Lip and Palate Patients: Accuracy Evaluation and Clinical Outcome
- 1.19 Novel 3D MRI Technique to Measure Perineal Membrane Structural Changes With Pregnancy and Childbirth: Technique Development and Measurement Feasibility
- 1.20 A Supplemental Technique for Preoperative Evaluation of Giant Intracranial Aneurysm
- 1.21 Maxillary Dentoskeletal Outcomes of the Expander With Differential Opening and the Fan-Type Expander: A Randomized Controlled Trial
- 1.22 Utility of Machine Learning of Apparent Diffusion Coefficient (ADC) and T2-Weighted (T2W) Radiomic Features in PI-RADS Version 2.1 Category 3 Lesions to Predict Prostate Cancer Diagnosis
- 1.23 Optimized Fitting of a Midface Implant to Anchor a Magnetic Nasal Prosthesis Using 3D Printing
- 1.24 Pars Triangularis Volume Asymmetry and Schneiderian First Rank Symptoms in Antipsychotic-naïve Schizophrenia
- 1.25 Stability and Reproducibility of Radiomic Features Based Various Segmentation Technique on MR Images of Hepatocellular Carcinoma (HCC)
- 1.26 Postsurgical Stability of Temporomandibular Joint of Skeletal Class III Patients Treated with 2-Jaw Orthognathic Surgery via Computer-Aided Three-Dimensional Simulation and Navigation in Orthognathic Surgery (CASNOS)
- 1.27 Performances of Whole Tumor Texture Analysis Based on MRI: Predicting Preoperative T Stage of Rectal Carcinomas
- 1.28 MONAI Expands its Horizons with Healthcare Imaging Annotation
- 1.29 Transcanal Computed Tomography Views for Transcanal Endoscopic Lateral Skull Base Surgery: Pilot Cadaveric Study.
- 1.30 Fusion of Subarachnoid Hemorrhage Data and Computed Tomography Angiography Data Is Helpful to Identify the Rupture Source in Patients With Multiple Intracranial Aneurysms
- 1.31 Assessment of Pulp Volume Changes After Surgically Assisted Rapid Palatal Expansion
- 1.32 Association of Regional White Matter Hyperintensity Volumes with Cognitive Dysfunction and Vascular Risk Factors In Patients With Amnestic Mild Cognitive Impairment
- 1.33 Association Between Tumor Size and Peritumoral Brain Edema in Patients With Convexity and Parasagittal Meningiomas
- 1.34 A New Method to Determine the Optimal Orientation of Slim Modiolar Cochlear Implant Electrode Array Insertion
- 1.35 Impact of the Craniofacial Surgery Simulation in Anterior Plagiocephaly on Orbits and Oculomotor Muscles: Biomechanical Analysis With a Finite Element Model
- 1.36 Comparing Three-Dimensional Models of Placenta Accreta Spectrum With Surgical Findings
- 1.37 Structural Failure Sites in Posterior Vaginal Wall Prolapse: Stress 3D MRI-Based Analysis
- 1.38 Long-Term Stability and Condylar Remodeling After Mandibular Advancement: A 5-Year Follow-Up
- 1.39 The Development of Novel 2-in-1 Patient-Specific, 3D-Printed Laminectomy Guides with Integrated Pedicle Screw Drill Guides
- 1.40 Creating a Cross-Sectional, CT and MR Atlas of the Pannon Minipig.
- 1.41 Optimization of Manufacturing Parameters and Tensile Specimen Geometry for Fused Deposition Modeling (FDM) 3D-Printed PETG
- 1.42 The Use of Cochlear-Enhancement Imaging to Predict Hearing Preservation Following Vestibular Schwannoma Removal
- 1.43 Manual Versus Semiautomatic Segmentation of Soft-Tissue Sarcomas on Magnetic Resonance Imaging: Evaluation of Similarity and Comparison of Segmentation Times
- 1.44 Comparing the Inter-Observer Reliability of the Tada Formula Among Neurosurgeons While Estimating the Intracerebral Haematoma Volume
- 1.45 Post-Discharge Chest CT Findings and Pulmonary Function Tests in Severe COVID-19 Patients
- 1.46 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?
- 1.47 Novel 3D MRI Technique to Measure Perineal Membrane Structural Changes With Pregnancy and Childbirth: Technique Development and Measurement Feasibility
- 1.48 Radiomic Machine Learning Classifiers in Spine Bone Tumors: A Multi-Software, Multi-Scanner Study
- 1.49 Virtual Planning and CAD/CAM-Assisted Distraction for Maxillary Hypoplasia in Cleft Lip and Palate Patients: Accuracy Evaluation and Clinical Outcome
- 1.50 The Topology of Ventricle Surfaces and Its Application in the Analysis of Hydrocephalic Ventricles: A Proof-of-Concept Study
- 1.51 Wearable Mixed-Reality Holographic Navigation Guiding the Management of Penetrating Intracranial Injury Caused by a Nail
- 1.52 BreastImplantAnalyzer: An Easy-to-Use, Validated Tool for Calculating Breast Implant Volume From MRI Data
- 1.53 Application of 3D Modeling and Fusion Technology of Medical Image Data in Image Teaching
- 1.54 Radiomics Analysis for Predicting Pembrolizumab Response in Patients With Advanced Rare Cancers
- 1.55 Three-Dimensional Evaluation of Maxillary Second Molar Position in Untreated Patients With Normal Occlusion: Implications for Preadjusted Appliance Prescriptions
- 1.56 3D Printing of Rapid, Low-Cost and Patient-Specific Models of Brain Vasculature for Use in Preoperative Planning in Clipping of Intracranial Aneurysms
- 1.57 Early Prediction of Putamen Imaging Features in HIV-Associated Neurocognitive Impairment Syndrome
- 1.58 Use of Volumetric CT Scanning to Predict Tumor Staging and Survival in Pancreatic Cancer Patients That Are to Be Administered Curative Resection
- 1.59 Fitting Unbranching Skeletal Structures to Objects
- 1.60 Three-Dimensional Modeling and Automatic Analysis of the Human Nasal Cavity and Paranasal Sinuses Using the Computational Fluid Dynamics Method
- 1.61 Comparison Between Computed Tomography and Silicone-Casting Methods to Determine Gunshot Cavities in Ballistic Soap
- 1.62 A Machine Learning-Based Radiomics Model for the Prediction of Axillary Lymph-Node Metastasis in Breast Cancer
- 1.63 Cost-Effective Fetal Lung Volumetry for Assessment of Congenital Diaphragmatic Hernia
- 1.64 The Role of Recipient Myosteatosis in Graft and Patient Survival After Deceased Donor Liver Transplantation
- 1.65 3D-Assisted Mandibular Reconstruction: A Technical Note of Fibula Free Flap With Preshaped Titanium Plate
- 1.66 Radiomics Approaches for Predicting Liver Fibrosis With Nonenhanced T1 -Weighted Imaging: Comparison of Different Radiomics Models
- 1.67 Clinical 3D Imaging of the Anterior Segment With Ultrasound Biomicroscopy
- 1.68 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
- 1.69 An Open-Source Three-Dimensionally Printed Laryngeal Model for Injection Laryngoplasty Training
- 1.70 Treatment Measures of Hemimandibular Hyperplasia and Associated Facial Deformities
- 1.71 Three-Dimensional Evaluation of Dental Decompensation and Mandibular Symphysis Remodeling on Orthodontic-Surgical Treatment of Class III Malocclusion
- 1.72 A CT-Based Radiomics Nomogram for Distinguishing Between Benign and Malignant Bone Tumours
- 1.73 A Supplemental Technique for Preoperative Evaluation of Giant Intracranial Aneurysm
- 1.74 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
- 1.75 Positron Emission Tomography-Based Short-Term Efficacy Evaluation and Prediction in Patients With Non-Small Cell Lung Cancer Treated With Hypo-Fractionated Radiotherapy
- 1.76 Radiomics-Based Machine Learning Model to Predict Risk of Death Within 5-Years in Clear Cell Renal Cell Carcinoma Patients
- 1.77 Exploring the Variability of Radiomic Features of Lung Cancer Lesions on Unenhanced and Contrast-Enhanced Chest CT Imaging
- 1.78 Regenerative Orthodontics: GBR and Corticotomy to Stretch the Limits of Orthodontic Treatment
- 1.79 The Effects of Age and Race on Calvarium, Tegmen, and Zygoma Thickness
- 1.80 Novel Workflow for Conversion of Catheter-Based Electroanatomic Mapping to DICOM Imaging for Noninvasive Radioablation of Ventricular Tachycardia
- 1.81 Deformation of the Pelvic Arteries Caused by Pneumoperitoneum and Postural Changes in an Animal Model
- 1.82 Development and Validation of a CT-Based Nomogram for Preoperative Prediction of Clear Cell Renal Cell Carcinoma Grades
- 1.83 CardIAc: An Open-Source Application for Myocardial Strain Analysis
- 1.84 Endoscope-Assisted Fluorescence-Guided Resection Allowing Supratotal Removal in Glioblastoma Surgery
- 1.85 Clinical and Radiological Predictors of Epidermal Growth Factor Receptor Mutation in Nonsmall Cell Lung Cancer
- 1.86 A User-Friendly Protocol for Mandibular Segmentation of CBCT Images for Superimposition and Internal Structure Analysis
- 1.87 Development, Validation, and Pilot MRI Safety Study of a High-Resolution, Open Source, Whole Body Pediatric Numerical Simulation Model
- 1.88 Condylar Changes in Children with Posterior Crossbite after Maxillary Expansion: Tridimensional Evaluation
- 1.89 New Insights Into Intrinsic Foot Muscle Morphology and Composition Using Ultra-High-Field (7-Tesla) Magnetic Resonance Imaging
- 1.90 3D-Volume Rendering of the Pelvis With Emphasis on Paraurethral Structures Based on MRI Scans and Comparisons Between 3D Slicer and OsiriX®
- 1.91 Shape of the Cochlear Basal Turn: An Indicator for an Optimal Electrode-to-Modiolus Proximity With Precurved Electrode Type
- 1.92 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
- 1.93 Impact of 3D Printing in Surgical Planning of Congenital Heart Disease
- 1.94 Association of White Matter Hyperintensity Progression with Cognitive Decline in Patients with Amnestic Mild Cognitive Impairment
A Multicontrast MR Atlas of the Wistar Rat Brain
Publication: Neuroimage. 2021 Nov 15;242:118470. PMID: 34391877 | PDF
Authors: Johnson GA, Laoprasert R, Anderson RJ, Cofer G, Cook J, Pratson F, White LE.
Institution: Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA.
Abstract: We describe a multi-contrast, multi-dimensional atlas of the Wistar rat acquired at microscopic spatial resolution using magnetic resonance histology (MRH). Diffusion weighted images, and associated scalar images were acquired of a single specimen with a fully sampled Fourier reconstruction, 61 angles and b=3000 s/mm2 yielding 50 um isotropic spatial resolution. The higher angular sampling allows use of the GQI algorithm improving the angular invariance of the scalar images and yielding an orientation distribution function to assist in delineating subtle boundaries where there are crossing fibers and track density images providing insight into local fiber architecture. A multigradient echo image of the same specimen was acquired at 25 um isotropic spatial resolution. A quantitative susceptibility map enhances fiber architecture relative to the magnitude images. An accompanying multi-specimen atlas (n=6) was acquired with compressed sensing with the same diffusion protocol as used for the single specimen atlas. An average was created using diffeomorphic mapping. Scalar volumes from the diffusion data, a T2* weighted volume, a quantitative susceptibility map, and a track density volume, all registered to the same space provide multiple contrasts to assist in anatomic delineation. The new template provides significantly increased contrast in the scalar DTI images when compared to previous atlases. A compact interactive viewer based on 3D Slicer is provided to facilitate comparison among the contrasts in the multiple volumes. The single volume and average atlas with multiple 3D volumes provide an improved template for anatomic interrogation of the Wistar rat brain. The improved contrast to noise in the scalar DTI images and the addition of other volumes (eg. QA,QSM,TDI ) will facilitate automated label registration for MR histology and preclinical imaging.
Methods for Intratumoral Microdialysis Probe Targeting and Validation in Murine Brain Tumor Models
Authors: Rajani K, Olson I, Jacobs JJ, Riviere-Cazaux C, Burns K, Carlstrom L, Schroeder M, Oh J, Howe CL, Rahman M, Sarkaria JN, Elmquist WF, Burns TC.
Institution: Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA.
Abstract: Background: Microdialysis is a well validated sampling technique that can be used for pharmacokinetic studies of oncological drugs targeting the central nervous system. This technique has also been applied to evaluate tumor metabolism and identify pharmacodynamic biomarkers of drug activity. Despite the potential utility of microdialysis for therapeutic discovery, variability in tumor size and location hamper routine use of microdialysis as a preclinical tool. Quantitative validation of microdialysis membrane location relative to radiographically evident tumor regions could facilitate rigorous preclinical studies. However, a widely accessible standardized workflow for preclinical catheter placement and validation is needed.
New method: We provide methods for a workflow to yield tailored placement of microdialysis probes within a murine intracranial tumor and illustrate in an IDH1-mutant patient-derived xenograft (PDX) model. This detailed workflow uses a freely available on-line tool built within 3D Slicer freeware to target microdialysis probe placement within the tumor core and validate probe placement fully within the tumor.
Results: We illustrate use of this workflow to validate microdialysis probe location relative to implanted IDH1-mutant PDXs, using the microdialysis probes to quantify levels of extracellular onco-metabolite D-2 hydroxyglutarate.
Comparison with existing methods: Previous methods have used 3D Slicer to reliably measure tumor volumes. Prior microdialysis studies have targeted expected tumor locations without validation.
Conclusions: The new method offers a streamlined and freely available workflow in 3D Slicer to optimize and validate microdialysis probe placement within a murine brain tumor.
Testing the Reliability of CT Scan-Based Dental Wear Magnitude Scoring
Authors: Godinho RM, Gonçalves C.
Institution: Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArHEB), Faculdade das Ciências Humanas e Sociais, Universidade do Algarve, Campus Gambelas, Faro, Portugal.
Abstract: Objectives: Digital models are now frequently used in biological anthropology (bioanthropology) research. Despite several studies validating this type of research, none has examined if the assessment of dental wear magnitude based on Computerized Tomography (CT) scans is reliable. Thus, this study aims to fill this gap and assess if dental wear magnitude scoring based on CT scans provides results consistent with scoring based on direct observation of the physical specimens.
Materials and methods: Dental wear magnitude from 412 teeth of 35 mandibles originating from the Portuguese Muge and Sado Mesolithic shell-middens was scored. The mandibles were also CT scanned and visualized using 3D Slicer. CT scan-based scoring of dental wear magnitude was then undertaken. Two scoring rounds were undertaken for each observation method (totaling four scoring rounds) and an intra-observer error test was performed. The averaged results of the two observation methods were compared via boxplots with paired cases.
Results: Intra-observer error was negligible and non-significant. Scoring results are comparable between the two observation methods. Notwithstanding, some differences were found, in which CT scan assessment generally overestimates dental wear when compared to direct observation.
Discussion: Our results generally validate the use of CT scans in studies of dental wear magnitude. Notwithstanding several caveats relating to CT scanning and visualization limitations should be considered to avoid over or under-estimation of dental wear.
The Topology of Ventricle Surfaces and Its Application in the Analysis of Hydrocephalic Ventricles: A Proof-of-Concept Study
Authors: Lo YT, Kumar S, Tan LQ, Lock C, Keong NCH.
Institution: Department of Neurosurgery, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore.
Abstract: Purpose: The cerebral ventricles deform in a non-uniform fashion in response to increased CSF volume and/or pressure in hydrocephalic syndromes. Current research is focused on volumetric analyses, while topological analysis of ventricular surfaces remains understudied. We developed a method of quantitatively modeling the curvature of ventricular surfaces to analyze changes in ventricular surfaces in normal pressure hydrocephalus (NPH) and Alzheimer's disease (AD), using the left frontal horn as an example.
Methods: 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. Next, the mean curvatures at a set of points on the ventricular surface were determined. The frontal horns were scaled and centered into normalized volumes, allowing for pooling across the study subjects. The frontal horn was divided into superolateral, superomedial, inferolateral, and inferomedial surfaces, and locoregional mean curvatures were analyzed. Statistical comparisons were made between NPH, AD, and HC groups.
Results: Significant differences in the mean curvature of lateral surfaces of the ventricles distinguished patterns of distortion between all three cohorts. Significant flattening of the superomedial surface discriminated NPH from HC and AD. However, significant rounding of the inferomedial surface compared to controls was a distinguishing feature of NPH alone.
Conclusion: NPH ventricles deform non-uniformly. The pattern of surface distortion may be used as an additional tool to differentiate between these hydrocephalic conditions.
Prediction of Locoregional Recurrence-Free Survival of Oesophageal Squamous Cell Carcinoma After Chemoradiotherapy Based on an Enhanced CT-Based Radiomics Model
Authors: Kong J, Zhu S, Shi G, Liu Z, Zhang J, Ren J.
Institution: Department of Radiation Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
Abstract: Background and purpose: Chemoradiotherapy is the standard treatment for moderate and advanced oesophageal cancer. The aim of this study was to establish a predictive model based on enhanced computed tomography examination, and to evaluate its clinical value for detecting locoregional recurrence-free survival (LRFS) in cases of oesophageal squamous cell carcinoma after radiotherapy.
Materials and methods: In total, 218 patients with pathologically diagnosed oesophageal squamous cell carcinoma who received radical chemoradiotherapy from July 2016 to December 2017 were collected in this study. Patients were randomly divided into either a training group (n=153) or a validation group (n=65) in a 7:3 ratio. Clinical patient information was then recorded. The enhanced computed tomography scan images of the patients were imported into 3D Slicer v.4.8.1, and the radiomic features were extracted by the Python programme package. In the training group, the dimensionality reduction of the radiomic features was implemented by Lasso regression, and then a radiological label, the model of predicting LRFS, was established and evaluated. To achieve a better prediction performance, the radiological label was combined with clinical risk factor information to construct a radiomics nomogram. A receiver operating characteristic curve was used to evaluate the efficacy of different models. Calibration curves were used to assess the consistency between the predicted and observed recurrence risk, and the Hosmer-Lemeshow method was used to test model fitness. The C-index evaluated the discriminating ability of the prediction model. Decision curve analysis was used to determine the clinical value of the constructed prediction model.
Results: Of the 218 patients followed up in this study, 44 patients (28.8%) in the training group and 21 patients (32.3%) in the validation group experienced recurrence. There was no difference in LRFS between the two groups (χ2 = 0.525, P=0.405). Lasso regression was used in the training group to select six significant radiomic features. The radiological label established using these six features had a satisfactory prediction performance. The C-index was 0.716 (95% CI: 0.645-0.787) in the training group and 0.718 (95% CI: 0.612-0.825) in the validation group. The radiomics nomogram, which included the radiological label and clinical risk factors, achieved a better prediction than the radiological label alone. The C-index was 0.742 (95% CI: 0.674-0.810) in the training group and 0.715 (95% CI: 0.609-0.820) in the validation group. The results of the calibration curve and decision curve analyses indicated that the radiomics nomogram was superior in predicting LRFS of oesophageal carcinoma after radiotherapy.
Conclusions: A radiological label was successfully established to predict the LRFS of oesophageal squamous cell carcinoma after radiotherapy. The radiomics nomogram was complementary to the clinical prognostic features and could improve the prediction of the LRFS after radiotherapy for oesophageal cancer.
Prediction of the Recurrence of Non-Functioning Pituitary Adenomas Using Preoperative Supra-Intra Sellar Volume and Tumor-Carotid Distance
Authors: Chen W, Wang M, Duan C, Yao S, Jiao H, Wang Z, Hu B, Mao Z, Zhu Y, Wang H.
Institution: Center for Pituitary Surgery, Department of Neurosurgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
Abstract: Background: Currently, it is difficult to estimate the possibility of recurrence of nonfunctioning pituitary adenomas (NFPAs). Markers such as Ki-67 or transcription factors rely on postoperative pathology, while few indices can be used for preoperative prediction. Therefore, we aimed to investigate the predictive effectiveness of supra-intrasellar volume and tumor-carotid distance based on measurements derived from preoperative magnetic resonance imaging (MRI) data.
Method: Ninety-eight cases of NFPAs were evaluated, along with their clinical characteristics and MRI features. Four radiologic indices were analyzed, including intrasellar tumor volume, suprasellar tumor volume, maximum horizontal tumor diameter, and intercarotid distance. The ratio of supra-intrasellar volume and ratio of tumor-carotid distance were measured using 3D Slicer software, and the sum of two ratios was defined as the V-D value. The correlation between recurrence and multiple factors was analyzed using univariate and multivariate logistic regression and Kaplan-Meier analysis, and ROC curves were used to estimate the prognostic performance of radiologic measurements in NFPAs.
Result: The supra-intrasellar volume ratio, tumor-carotid distance ratio and V-D value were significantly correlated with the recurrence of NFPAs. The predictive importance of the V-D value reached 84.5%, with a sensitivity of 83.7% and specificity of 67.3%. The cutoff limit of the V-D value was 1.53, and patients with V-D values higher than 1.53 tended to relapse much earlier.
Conclusion: The V-D value has predictive importance for the recurrence of NFPAs preoperatively. Patients with higher V-D values will undergo recurrence earlier and should be given greater consideration in terms of surgery and follow-up time.
Analysis of Changes in the Volume of Edema Around Brain Contusions and the Influencing Factors: A Single-Center, Retrospective, Observational Study
Authors: Liu HB, Xu WM, Wang SS, Wei LF, Hong JF, Wang C, Xian L.
Institution: Department of Neurosurgery of the 900th Hospital, Fuzong Clinical Medical School of Fujian Medical University, Fuzhou, Fujian Province, China.
Abstract: Traumatic brain injury (TBI), a common neurosurgical condition, has well-known treatment guidelines. However, the mechanisms underlying the varying severity of brain edema secondary to TBI are largely unknown, leading to controversial treatments.This study seeks to measure edema volumes around brain contusions in different regions, analyze factors related to differences in edema volume and provide a theoretical basis for brain edema treatment.Data from 113 brain contusion patients treated at the Department of Neurosurgery of Fuzhou General Hospital from January 2017 to November 2019 were analyzed retrospectively. Based on computed tomography (CT) data, the patients were divided into the venous group (brain contusion in regions with large cortical veins, n = 47) and the nonvenous group (brain contusions in other regions, n = 66). Here, 3D Slicer software was used to calculate the brain contusion volume on the first CT obtained after injury and the brain contusion volume and its surrounding edema on the 5th day after injury. The brain contusion volume to surrounding edema volume ratio was calculated, and the number of patients who showed brain contusion progression requiring surgery was determined. Hematocrit (Hct), fibrinogen (Fg), and d-dimer levels within 6 hours and on the 5th day after admission were also compared.Patients in the venous group had a significantly increased percentage of area with edema around the brain contusion compared with patients in the nonvenous group (P < .05), and the 2 groups showed no significant difference in the number of patients with brain contusion progression or surgical treatment (P > .05) or Hct, Fg, or d-dimer (D-D) levels. For all patients, Hct, Fg, and D-D levels within 6 hours after admission were significantly different from those on the 5th day (P < .05 for all).Cortical venous obstruction may be the most important factor influencing edema around brain contusions. The Fg level decreased slightly, and the D-D level increased to its peak rapidly after mild-moderate TBI. This change was followed by a gradual increase in the former and a gradual decrease in the latter.
Hybrid Additive Fabrication of a Transparent Liver with Biosimilar Haptic Response for Preoperative Planning
Publication: Diagnostics (Basel). 2021 Sep 21;11(9):1734. PMID: 34574075 | PDF
Authors: Aseni P, Santaniello T, Rizzetto F, Gentili L, Pezzotta F, Cavaliere F, Vertemati M, Milani P.
Institution: Department of Emergency, ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy.
Abstract: Due to the complexity of liver surgery, the interest in 3D printing is constantly increasing among hepatobiliary surgeons. The aim of this study was to produce a patient-specific transparent life-sized liver model with tissue-like haptic properties by combining additive manufacturing and 3D moulding. A multistep pipeline was adopted to obtain accurate 3D printable models. Semiautomatic segmentation and registration of routine medical imaging using 3D Slicer software allowed to obtain digital objects representing the structures of interest (liver parenchyma, vasculo-biliary branching, and intrahepatic lesion). The virtual models were used as the source data for a hybrid fabrication process based on additive manufacturing using soft resins and casting of tissue-mimicking silicone-based blend into 3D moulds. The model of the haptic liver reproduced with high fidelity the vasculo-biliary branching and the relationship with the intrahepatic lesion embedded into the transparent parenchyma. It offered high-quality haptic perception and a remarkable degree of surgical and anatomical information. Our 3D transparent model with haptic properties can help surgeons understand the spatial changes of intrahepatic structures during surgical manoeuvres, optimising preoperative surgical planning.
The Impact of Tumor Edema on T2-Weighted 3T-MRI Invasive Breast Cancer Histological Characterization: A Pilot Radiomics Study
Publication: Cancers (Basel). 2021 Sep 15;13(18):4635. PMID: 34572862 | PDF
Authors: Santucci D, Faiella E, Cordelli E, Calabrese A, Landi R, de Felice C, Beomonte Zobel B, Grasso RF, Iannello G, Soda P.
Institution: Department of Radiology, University of Rome "Campus Bio-Medico", Roma, Italy.
Abstract: Background: to evaluate the contribution of edema associated with histological features to the prediction of breast cancer (BC) prognosis using T2-weighted MRI radiomics.
Methods: 160 patients who underwent staging 3T-MRI from January 2015 to January 2019, with 164 histologically proven invasive BC lesions, were retrospectively reviewed. Patient data (age, menopausal status, family history, hormone therapy), tumor MRI-features (location, margins, enhancement) and histological features (histological type, grading, ER, PgR, HER2, Ki-67 index) were collected. Of the 160 MRI exams, 120 were considered eligible, corresponding to 127 lesions. T2-MRI were used to identify edema, which was classified in four groups: peritumoral, pre-pectoral, subcutaneous, or diffuse. A semi-automatic segmentation of the edema was performed for each lesion, using 3D Slicer open-source software. Main radiomics features were extracted and selected using a wrapper selection method. A Random Forest type classifier was trained to measure the performance of predicting histological factors using semantic features (patient data and MRI features) alone and semantic features associated with edema radiomics features.
Results: edema was absent in 37 lesions and present in 127 (62 peritumoral, 26 pre-pectoral, 16 subcutaneous, 23 diffuse). The AUC-classifier obtained by associating edema radiomics with semantic features was always higher compared to the AUC-classifier obtained from semantic features alone, for all five histological classes prediction (0.645 vs. 0.520 for histological type, 0.789 vs. 0.590 for grading, 0.487 vs. 0.466 for ER, 0.659 vs. 0.546 for PgR, and 0.62 vs. 0.573 for Ki67).
Conclusions: radiomic features extracted from tumor edema contribute significantly to predicting tumor histology, increasing the accuracy obtained from the combination of patient clinical characteristics and breast imaging data.
A Comparative Study Between State-of-the-Art MRI Deidentification and AnonyMI, a New Method Combining Re-Identification Risk Reduction and Geometrical Preservation
Publication: Hum Brain Mapp. 2021 Sep 14 PMID: 34520074
Authors: Mikulan E, Russo S, Zauli FM, d'Orio P, Parmigiani S, Favaro J, Knight W, Squarza S, Perri P, Cardinale F, Avanzini P, Pigorini A.
Institution: Dipartimento di Scienze Biomediche e Cliniche "L.Sacco", Università degli Studi di Milano, Milano, Italy.
Abstract: Deidentifying MRIs constitutes an imperative challenge, as it aims at precluding the possibility of re-identification of a research subject or patient, but at the same time it should preserve as much geometrical information as possible, in order to maximize data reusability and to facilitate interoperability. Although several deidentification methods exist, no comprehensive and comparative evaluation of deidentification performance has been carried out across them. Moreover, the possible ways these methods can compromise subsequent analysis has not been exhaustively tested. To tackle these issues, we developed AnonyMI, a novel MRI deidentification method, implemented as a user-friendly 3D Slicer plugin-in, which aims at providing a balance between identity protection and geometrical preservation. To test these features, we performed two series of analyses on which we compared AnonyMI to other two state-of-the-art methods, to evaluate, at the same time, how efficient they are at deidentifying MRIs and how much they affect subsequent analyses, with particular emphasis on source localization procedures. Our results show that all three methods significantly reduce the re-identification risk but AnonyMI provides the best geometrical conservation. Notably, it also offers several technical advantages such as a user-friendly interface, multiple input-output capabilities, the possibility of being tailored to specific needs, batch processing and efficient visualization for quality assurance.
Three-Dimensional Structure of the Basal Lamella of the Middle Turbinate
Authors: Eördögh M, Baksa G, Grimm A, Bárány L, Petneházy Ö, Reisch R, Schroeder HWS, Briner HR, Hosemann W.
Institution: Department of Neurosurgery, University Medicine Greifswald, Sauerbruchstraße, Greifswald, Germany.
Abstract: The middle turbinate's basal lamella (3BL) is a variable landmark which needs to be understood in endoscopic transnasal skull base surgery. It comprises an anterior frontal and a posterior horizontal part and appears in its simplest depiction to be "L"-shaped, when viewed laterally. In this study we analyzed its 3D morphology and variations focusing on a precise and systematic description of the anatomy. CBCTs of 25 adults, 19 cadavers and 6 skulls (total: 100 sides) were investigated with the 3D Slicer software, creating 3D models of the 3BL. We introduced a novel geometrical classification of the 3BL's shape, based on segments. We analyzed their parameters and relationship to neighboring structures. When viewed laterally, there was no consistent "L"-shaped appearance of the 3BL, as it is frequently quoted. A classification of 9 segment types was used to describe the 3BL. The 3BLs had in average of 2.95 ± 0.70 segments (median: 3), the most frequent was the horizontal plate (23.05% of all segments), next a concave/convex plate (22.71%), then a sigma plate (22.37%). Further types were rare. We identified a horizontal plate in 68% of all lateral views whilst 32% of the 3BLs were vertical. A sigma-concave/convex-horizontal trisegmental 3BL was the most common phenotype (27%). Globally, the sigma-concave/convex pattern was present in 42%. The 3BL adhered the ethmoidal bulla in 87%. The segmenting method is eligible to describe the 3BL's sophisticated morphology.
Flatness of the Meckel Cave May Cause Primary Trigeminal Neuralgia: A Radiomics-Based Study
Publication: J Headache Pain. 2021 Sep 3;22(1):104. PMID: 34479476 | PDF
Authors: Lin J, Zhang Y, Li W, Yan J, Ke Y.
Institution: Department of Neurosurgery, Guangdong Second Provincial General Hospital, Guangzhou, China.
Abstract: Background: Neurovascular contact (NVC) is the main cause of primary trigeminal neuralgia (PTN); however, cases of PTN without NVC are still observed. In this study, the Meckel cave (MC) morphology in PTN were analyzed by radiomics and compared to healthy controls (HCs) to explore the cause of PTN.
Methods: We studied the 3.0T MRI data of 115 patients with PTN and 46 HCs. Bilateral MC was modeled using the 3D Slicer software, and the morphological characteristics of MC were analyzed using the radiomics method.
Results: The right side incidence rate in the PTN group was higher than the left side incidence. By analyzing the flatness feature of MC, we observed that the affected side of the PTN was lower than that of the unaffected side, the right MC of the PTN and HC was lower than that of the left MC, the MC of the affected side of the left and right PTN without bilateral NVC was lower than that of the unaffected side.
Conclusions: By providing a method to analyze the morphology of the MC, we found that there is an asymmetry in the morphology of bilateral MC in the PTN and HC groups. It can be inferred that the flatness of the MC may be a cause of PTN.
An Unsupervised Learning Approach to Ultrasound Strain Elastography With Spatio-Temporal Consistency
Publication: Phys Med Biol. 2021 Sep 3;66(17):175031. PMID: 34298531 | PDF
Authors: Delaunay R, Hu Y, Vercauteren T.
Institution: Wellcome/EPSRC Centre for Interventional and Surgical Sciences, University College London, London, UK.
Abstract: Quasi-static ultrasound elastography (USE) is an imaging modality that measures deformation (i.e. strain) of tissue in response to an applied mechanical force. In USE, the strain modulus is traditionally obtained by deriving the displacement field estimated between a pair of radio-frequency data. In this work we propose a recurrent network architecture with convolutional long-short-term memory decoder blocks to improve displacement estimation and spatio-temporal continuity between time series ultrasound frames. The network is trained in an unsupervised way, by optimising a similarity metric between the reference and compressed image. Our training loss is also composed of a regularisation term that preserves displacement continuity by directly optimising the strain smoothness, and a temporal continuity term that enforces consistency between successive strain predictions. In addition, we propose an open-accessin vivodatabase for quasi-static USE, which consists of radio-frequency data sequences captured on the arm of a human volunteer. Our results from numerical simulation andin vivodata suggest that our recurrent neural network can account for larger deformations, as compared with two other feed-forward neural networks. In all experiments, our recurrent network outperformed the state-of-the-art for both learning-based and optimisation-based methods, in terms of elastographic signal-to-noise ratio, strain consistency, and image similarity. Finally, our open-source code provides a 3D Slicer visualisation module that can be used to process ultrasound RF frames in real-time, at a rate of up to 20 frames per second, using a standard GPU.
A Mandible with the Temporomandibular Joint-A New FEM Model Dedicated to Strength and Fatigue Calculations of Bonding Elements Used in Fracture and Defect Surgery
Publication: Materials (Basel). 2021 Sep 2;14(17):5031. PMID: 34501120 | PDF
Authors: Mańkowski J, Piękoś J, Dominiak K, Klukowski P, Fotek M, Zawisza M, Żach P.
Institution: Institute of Machine Design Fundamentals, Warsaw University of Technology, Warsaw, Poland.
Abstract: The aim of the study was to develop a new FEM (finite element method) model of a mandible with the temporal joint, which can be used in the numerical verification of the work of bonding elements used in surgical operations of patients with mandibular fractures or defects. Most of such types of numerical models are dedicated to a specific case. The authors engaged themselves in building a model that can be relatively easily adapted to various types of tasks, allowing to assess stiffness, strength and durability of the bonded fragments, taking into account operational loads and fatigue limit that vary in time. The source of data constituting the basis for the construction of the model were DICOM (digital imaging and communications in medicine) files from medical imaging using computed tomography. On their basis, using the 3D Slicer program and algorithms based on the Hounsfield scale, a 3D model was created in the STL (standard triangle language) format. A CAD (computer-aided design) model was created using VRMesh and SolidWorks. An FEM model was built using HyperWorks and Abaqus/CAE. Abaqus solver was used for FEM analyses. A model meeting the adopted assumptions was built. The verification was conducted by analyzing the influence of the simplifications of the temporomandibular joint in the assessment of mandibular strain. The work of an undamaged mandible and the work of the bonded fracture of the mandible were simulated.
Mini Hyrax vs Hyrax Expanders in the Rapid Palatal Expansion in Adolescents With Posterior Crossbite: A Randomized Controlled Clinical Trial
Authors: Silveira GS, Abreu LG, Palomo JM, da Matta Cid Pinto LS, de Sousa AA, Gribel BF, Oliveira DD.
Institution: School of Dentistry, Pontifical Catholic University of Minas Gerais, Belo Horizonte, MG, Brazil.
Abstract: Purpose: The aim of this study was to compare the dental effects, impact on quality of life, and pain perception of adolescents wearing Mini Hyrax and Hyrax expanders in rapid palatal expansion.
Methods: Thirty-four adolescents aged 11 to 16 years, with maxillary transverse deficiency (unilateral or bilateral posterior crossbite), were randomly allocated into two groups, Mini Hyrax group and Hyrax group (1:1 ratio). Dental effects were evaluated by digitally superimposed pretreatment and postretention three-dimensional intraoral scans on the palatal rugaes using the software 3D Slicer. Impact on quality of life was assessed with the OHIP-14 questionnaire applied in the pretreatment, posttreatment and postretention. Visual analog scale was applied 24, 48, and 72 h and 7 days after the first activation of the expander.
Results: Thirty of the 34 adolescents recruited completed the study. There were no statistically significant differences in dentoalveolar effects between groups. OHIP-14 scores across time among Mini Hyrax wearers were similar to those of the Hyrax wearers. The inter-group comparisons showed no difference between groups with respect to the OHIP-14 scores in posttreatment and postretention (p > 0.05). There were no differences in pain perception between groups. Considering intra-group comparison, the reduction in pain perception among adolescents in the Mini Hyrax group was gradual. Among adolescents in the Hyrax group, a statistically significant reduction between 48 and 72 h was observed.
Conclusion: There were no significant differences in dental effects, impact on quality of life and pain perception between adolescents wearing Mini Hyrax and Hyrax expanders in rapid palatal expansion.
Authors: Gao Y, Wang H, Tu P, Hu J, Wang Q, Chen X.
Institution: School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai, China.
Abstract: Background: The accurate distal locking of intramedullary (IM) nails is a clinical challenge for surgeons. Although many navigation systems have been developed, a real-time guide method with free radiation exposure, better user convenience, and high cost performance has not been proposed.
Methods: This paper aims to develop an electromagnetic navigation system named TianXuan-MDTS that provides surgeons with a proven surgical solution. And the registration method with external landmarks for IM nails and calibration algorithm for guiders were proposed. A puncture experiment, model experiments measured by 3D Slicer and cadaver experiments (2 cadaveric leg specimens and 6 drilling operations) are conducted to evaluate its performance and stability.
Results: The registration deviations (TRE) is 1.05± 0.13 mm. In the puncture experiment, a success rate of 96% can be achieved in 45.94 s. TianXuan-MDTS were evaluated on 3 tibia model. The results demonstrated that all 9 screw holes were successfully prepared at a rate of 100% in 91.67 s. And the entry point, end point, and angular deviations were 1.60±0.20 mm, 1.47±0.18 mm, and 3.10±0.84°, respectively. Postoperative fluoroscopy in cadaver experiments showed that all drills were in the distal locking holes, with a success rate of 100% and the average time 143.17± 18.27s.
Conclusions: The experimental results indicate that our system with novel registration and calibration methods could serve as a feasible and promising tool to assist surgeons during distal locking.
TorchIO: A Python Library for Efficient Loading, Preprocessing, Augmentation and Patch-Based Sampling of Medical Images in Deep Learning
Authors: Pérez-García F, Sparks R, Ourselin S.
Institution: Department of Medical Physics and Biomedical Engineering, University College London, UK.
Abstract: Background and objective: Processing of medical images such as MRI or CT presents different challenges compared to RGB images typically used in computer vision. These include a lack of labels for large datasets, high computational costs, and the need of metadata to describe the physical properties of voxels. Data augmentation is used to artificially increase the size of the training datasets. Training with image subvolumes or patches decreases the need for computational power. Spatial metadata needs to be carefully taken into account in order to ensure a correct alignment and orientation of volumes.
Methods: We present TorchIO, an open-source Python library to enable efficient loading, preprocessing, augmentation and patch-based sampling of medical images for deep learning. TorchIO follows the style of PyTorch and integrates standard medical image processing libraries to efficiently process images during training of neural networks. TorchIO transforms can be easily composed, reproduced, traced and extended. Most transforms can be inverted, making the library suitable for test-time augmentation and estimation of aleatoric uncertainty in the context of segmentation. We provide multiple generic preprocessing and augmentation operations as well as simulation of MRI-specific artifacts.
Results: Source code, comprehensive tutorials and extensive documentation for TorchIO can be found at http://torchio.rtfd.io/. The package can be installed from the Python Package Index (PyPI) running pip install torchio. It includes a command-line interface which allows users to apply transforms to image files without using Python. Additionally, we provide a graphical user interface within a TorchIO extension in 3D Slicer to visualize the effects of transforms.
Conclusion: TorchIO was developed to help researchers standardize medical image processing pipelines and allow them to focus on the deep learning experiments. It encourages good open-science practices, as it supports experiment reproducibility and is version-controlled so that the software can be cited precisely. Due to its modularity, the library is compatible with other frameworks for deep learning with medical images.
Virtual Planning and CAD/CAM-Assisted Distraction for Maxillary Hypoplasia in Cleft Lip and Palate Patients: Accuracy Evaluation and Clinical Outcome
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 and Geomagic Wrap to evaluate the accuracy of maxillary repositioning and assess 3D bone changes. Clinical outcome was evaluated at the 1-year follow-up (T2). The patients and surgeon were satisfied with the occlusal and aesthetic outcomes. A maximum difference of 2 mm between the VSP and the actual surgical outcome was chosen as the success criterion for accuracy. The average linear difference for selected points was <2 mm in four patients and >2 mm in two patients. The average distance of the postoperative maxilla from the VSP model was 2.28 mm (median 1.85), while the average forward movement of the maxilla was 10.18 mm The protocol used is effective and accurate in the correction of severe maxillary hypoplasia in CLP patients. Early removal of the distractor and stabilization with plates reduces patient discomfort and does not jeopardize stability. This protocol should be reserved for complex cases due to the costs of the procedure, which are not negligible.
Novel 3D MRI Technique to Measure Perineal Membrane Structural Changes With Pregnancy and Childbirth: Technique Development and Measurement Feasibility
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.
Results: Model reconstruction was similar to cadaver dissection findings. Morphological measurements were feasible in all women (NP, n = 10; CS, n = 6; VD, n = 19). Swinging door angle was 13o greater in CD (p = 0.03; d = 1.15) and 16o greater in VD (p < 0.001; d = 1.41) compared to NP. VD showed 13% larger separation at the perineal body than NP (p = 0.097, d = 0.84) and 23% larger hiatal area than CD (p = 0.14, d = 0.94).
Conclusion: This novel and anatomically validated MRI-based perineal membrane reconstruction technique is feasible. Preliminary findings show that pregnancy and childbirth both influence perineal membrane morphology with VD being associated with the largest swinging door angle and perineal body separation.
A Supplemental Technique for Preoperative Evaluation of Giant Intracranial Aneurysm
Authors: Wang HW, Wu C, Xue Z, Shu XJ, Sun ZH.
Institution: Chinese PLA General Hospital, Neurosurgery, Beijing, China.
Abstract: Background: 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.
Material and methods: Patients with GIAs who were treated with microsurgery in our department were included in this study. Both the TOF and MSDE sequence data for each patient were loaded into 3D Slicer for reconstruction and segmentation. The parameters measured by 3D Slicer were compared with those measured by DSA.
Results: The mean diameter for all GIAs was 28.7 ± 1.5 mm (range, 25.9-31.9 mm). The mean diameter for all GIAs measured by DSA and 3D Slicer was 24.46 ± 5.25 and 28.66 ± 1.48 mm, respectively (t = 4.948, p < 0.01). When only the nonthrombotic GIAs were included, the mean diameter measured by DSA and 3D Slicer was 28.69 ± 2.03 and 28.97 ± 1.79 mm, respectively (t = 1.023, p = 0.323). The mean aneurysmal volume was 8,292.6 ± 1,175.1 mm3 and the mean thrombotic volume was 3,590.0 ± 1,003.7 mm3.
Conclusion: The MSDE sequence brings diagnostic benefits as a comparison to other MRI sequences. Reconstruction of GIAs with 3D Slicer is a low-cost, dependable, and useful supplemental technique for surgical planning.
Maxillary Dentoskeletal Outcomes of the Expander With Differential Opening and the Fan-Type Expander: A Randomized Controlled Trial
Publication: Clin Oral Investig. 2021 Sep;25(9):5247-56. PMID: 33580351 | PDF
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, Bauru, SP, Brazil.
Abstract: Objectives: 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).
Results: The EDO group comprised 24 patients treated with the EDO (13 female, 11 male; 7.6 years). The FE group comprised 24 patients treated with the FE (14 female, 10 male; 7.8 years). Skeletal lateral displacements were greater in the EDO group with greater expansion in the orbital, nasal cavity, zygomatic bone, and palate regions (mean intergroup differences of 0.4, 0.8, 0.9, and 1.1 mm, respectively). Intercanine expansion and canine buccal inclination were greater in the FE group, while intermolar distance changes and molar buccal inclination were greater in the EDO group. Similar changes were observed for vertical and anteroposterior displacements and palatal plane rotation.
Conclusions: The EDO produced greater transverse skeletal expansion compared to the FE, with similar vertical and anteroposterior effects. Dental changes were greater in the molar region for patients treated with the EDO and in the canine region for patients treated with the FE.
Clinical relevance: The EDO and the FE are capable of producing skeletal changes in the mixed dentition. The decision between both expanders will depend on the amount of expansion required in the molar region and in the nasomaxillary complex.
Utility of Machine Learning of Apparent Diffusion Coefficient (ADC) and T2-Weighted (T2W) Radiomic Features in PI-RADS Version 2.1 Category 3 Lesions to Predict Prostate Cancer Diagnosis
Publication: Abdom Radiol (NY). 2021 Aug 31. PMID: 34467426
Authors: Lim CS, Abreu-Gomez J, Thornhill R, James N, Al Kindi A, Lim AS, Schieda N.
Institution: Department of Medical Imaging, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada.
Abstract: Purpose: To evaluate if machine learning (ML) of radiomic features extracted from apparent diffusion coefficient (ADC) and T2-weighted (T2W) MRI can predict prostate cancer (PCa) diagnosis in Prostate Imaging-Reporting and Data System (PI-RADS) version 2.1 category 3 lesions.
Methods: This multi-institutional review board-approved retrospective case-control study evaluated 158 men with 160 PI-RADS category 3 lesions (79 peripheral zone, 81 transition zone) diagnosed at 3-Tesla MRI with histopathology diagnosis by MRI-TRUS-guided targeted biopsy. A blinded radiologist confirmed PI-RADS v2.1 score and segmented lesions on axial T2W and ADC images using 3D Slicer, extracting radiomic features with an open-source software (Pyradiomics). Diagnostic accuracy for (1) any PCa and (2) clinically significant (CS; International Society of Urogenital Pathology Grade Group ≥ 2) PCa was assessed using XGBoost with tenfold cross -validation.
Results: From 160 PI-RADS 3 lesions, there were 50.0% (80/160) PCa, including 36.3% (29/80) CS-PCa (63.8% [51/80] ISUP 1, 23.8% [19/80] ISUP 2, 8.8% [7/80] ISUP 3, 3.8% [3/80] ISUP 4). The remaining 50.0% (80/160) lesions were benign. ML of all radiomic features from T2W and ADC achieved area under receiver operating characteristic curve (AUC) for diagnosis of (1) CS-PCa 0.547 (95% Confidence Intervals 0.510-0.584) for T2W and 0.684 (CI 0.652-0.715) for ADC and (2) any PCa 0.608 (CI 0.579-0.636) for T2W and 0.642 (CI 0.614-0.0.670) for ADC.
Conclusion: Our results indicate ML of radiomic features extracted from T2W and ADC achieved at best moderate accuracy for determining which PI-RADS category 3 lesions represent PCa.
Optimized Fitting of a Midface Implant to Anchor a Magnetic Nasal Prosthesis Using 3D Printing
Publication: HNO. 2021 Aug 31. PMID: 34463790
Authors: Wrobel C, Keppeler D, Meyer AC.
Institution: Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, Göttingen, Deutschland.
Abstract: Background: Plate-based anchorage systems for craniofacial prostheses offer advantages over extraoral solitary titanium implants in terms of the flexible choice of mounting points and higher stability. Disadvantages become apparent in the complex individual intraoperative adaptation of the plate-based systems to the usually poorly accessible bone. The current article presents a method to overcome these disadvantages and make greater use of the advantages of plate-based systems.
Materials and methods: The bony midface of a patient who had undergone rhinectomy for cancer of the nasal entrance was reconstructed as a virtual 3D model based on preoperative CT. The open-source software, 3D Slicer allowed easy and fast reconstruction as well as adaptation for 3D printing using transparent plastic (MED610; stratasys Ltd., MN, USA).
Results: A titanium mini-plate (MEDICON) for anchoring the nasal prosthesis could be fitted extremely precisely on the midface 3D print. Important anatomical structures were spared, and screw placement was selected according to the individual bone thickness. Implantation of the in-advance fitted titanium plate was performed without complications and without further adjustments.
Conclusion: In-advance fitting of plate-based systems for anchorage of craniofacial prostheses using 3D printing of the midface overcomes their disadvantages of time-consuming and possibly imprecise individual adaptation. This method further exploits the advantages of higher stability through more possible mounting points, even in thinner bone, to prevent loosening. In addition, in-advance fitting of titanium plates on the 3D model enables better identification and protection of important anatomical structures and shortens operative time.
Pars Triangularis Volume Asymmetry and Schneiderian First Rank Symptoms in Antipsychotic-naïve Schizophrenia
Authors: Shivakumar V, Sreeraj VS, Kalmady SV, Gangadhar BN, Venkatasubramanian G.
Institution: Department of Integrative Medicine, National Institute of Mental Health & NeuroSciences (NIMHANS), Bangalore, India.
Abstract: Objective: Schizophrenia is a disorder of language and self, with first-rank symptoms (FRS) as one of the predominant features in a subset of patients. Abnormal language lateralization is hypothesized to underlie the neurobiology of FRS in schizophrenia. The role of Broca's area with its right-hemispheric counterpart, consisting of pars triangularis (PTr) and pars opercularis (POp) of the inferior frontal gyrus in FRS is undetermined. We compared the volumes and asymmetries of PTr & POp in anti-psychotic-naive schizophrenia patients with FRS (FRS[＋]) with those without FRS (FRS[-]) and healthy-controls (HC) using three dimensional, interactive, semi-automated volumetric morphometry.
Methods: Antipsychotic naïve FRS(＋) (n = 27), FRS(-) (n = 24) and HC (n = 51) were carefully assessed with structured and semi-structured clinical tools. T1-weighted images were acquired in a 3T scanner. Volumes of regions of interest were measured independently for both sides using 3D Slicer software, and asymmetry indices were calculated.
Results: FRS(＋) but not FRS(-) had a significant volume deficit in right PTr after controlling for the potential confounding effects of age, sex, and intracranial volume (p = 0.029). There was a significant leftward asymmetry of PTr in patients with FRS (i.e., leftward asymmetry in patients) (p = 0.026). No significant volume/asymmetry abnormalities were observed in POp.
Conclusion: Study findings suggest reduced right PTr volume with leftward asymmetry to be associated with FRS in schizophrenia. This is consistent with the loss of Yakovlevian torque in schizophrenia. Role of PTr in the neurobiology of schizophrenia as a disorder of self, speech, and social cognition needs further systematic evaluation in future research.
Stability and Reproducibility of Radiomic Features Based Various Segmentation Technique on MR Images of Hepatocellular Carcinoma (HCC)
Authors: Haniff NSM, Abdul Karim MK, Osman NH, Saripan MI, Che Isa IN, Ibahim MJ.
Institution: Department of Physics, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
Abstract: Hepatocellular carcinoma (HCC) is considered as a complex liver disease and ranked as the eighth-highest mortality rate with a prevalence of 2.4% in Malaysia. Magnetic resonance imaging (MRI) has been acknowledged for its advantages, a gold technique for diagnosing HCC, and yet the false-negative diagnosis from the examinations is inevitable. In this study, 30 MR images from patients diagnosed with HCC is used to evaluate the robustness of semi-automatic segmentation using the flood fill algorithm for quantitative features extraction. The relevant features were extracted from the segmented MR images of HCC. Four types of features extraction were used for this study, which are tumour intensity, shape feature, textural feature and wavelet feature. A total of 662 radiomic features were extracted from manual and semi-automatic segmentation and compared using intra-class relation coefficient (ICC). Radiomic features extracted using semi-automatic segmentation utilized flood filling algorithm from 3D Slicer had significantly higher reproducibility (average ICC = 0.952 ± 0.009, p < 0.05) compared with features extracted from manual segmentation (average ICC = 0.897 ± 0.011, p > 0.05). Moreover, features extracted from semi-automatic segmentation were more robust compared to manual segmentation. This study shows that semi-automatic segmentation from 3D-Slicer is a better alternative to the manual segmentation, as they can produce more robust and reproducible radiomic features.
Publication: Biomed Res Int. 2021 Aug 6;2021:1563551. PMID: 34409098| PDF
Authors: Wang LC, Lee YH, Tsai CY, Wu TJ, Teng YY, Lai JP, Lin SS, Chang YJ.
Institution: Department of Craniofacial Orthodontics, Department of Dentistry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
Abstract: Objective: The aim of this study is to clarify the postsurgical stability of temporomandibular joints in skeletal class III patients treated with 2-jaw orthognathic surgery which was performed utilizing computer-aided three-dimensional simulation and navigation in orthognathic surgery (CASNOS) protocol.
Materials and methods: 23 consecutive nongrowing skeletal class III patients with mandibular prognathism associated with maxillary retrognathism treated with 2-jaw orthognathic surgery between 2018 and 2019 were enrolled in this study. The surgery was planned according to the standardized protocol of CASNOS (computer-aided three-dimensional simulation and navigation in orthognathic surgery). Computed tomography (CT) scans were performed in all patients 3 weeks presurgically and 6 months postsurgically. ITKSNAP and 3D Slicer software were used to reconstruct three-dimensional facial skeletal images, to carry out image segmentation, and to superimpose and quantify the TMJ position changes before and after surgery. Amount of displacement of the most medial and lateral points of the condyles and the change of intercondylar angles were measured to evaluate the postsurgical stability of TMJ.
Results: A total amount of 23 skeletal class III patients (female : male = 12 : 11) with age ranged from 20.3 to 33.5 years (mean: 24.39 ± 4.8 years old) underwent Le Fort I maxillary advancement and BSSO setback of the mandible. The surgical outcome revealed the satisfactory correction of their skeletal deformities. The mean displacement of the right most lateral condylar point (RL-RL') was 1.04 ± 0.42 mm and the mean displacement of the left most lateral condylar point (LL-LL') was 1.19 ± 0.41 mm. The mean displacement of the right most medial condylar point (RM-RM') was 1.03 ± 0.39 mm and the left most medial condylar point (LM-LM') was 0.96 ± 0.39 mm. The mean intercondylar angle was 161.61 ± 5.08° presurgically and 159.28 ± 4.92° postsurgically.
Conclusion: The postsurgical position of TM joint condyles in our study only presented a mild change with all the landmark displacement within a range of 1.2 mm. This indicates the bimaxillary orthognathic surgery via 3D CASNOS protocol can achieve a desired and stable result of TMJ position in treating skeletal class III adult patients with retrognathic maxilla and prognathic mandible.
Performances of Whole Tumor Texture Analysis Based on MRI: Predicting Preoperative T Stage of Rectal Carcinomas
Authors: You J, Yin J.
Institution: Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China.
Abstract: Objective: To determine whether there is a correlation between texture features extracted from high-resolution T2-weighted imaging (HR-T2WI) or apparent diffusion coefficient (ADC) maps and the preoperative T stage (stages T1-2 versus T3-4) in rectal carcinomas.
Materials and methods: One hundred and fifty four patients with rectal carcinomas who underwent preoperative HR-T2WI and diffusion-weighted imaging were enrolled. Patients were divided into training (n = 89) and validation (n = 65) cohorts. 3D Slicer was used to segment the entire volume of interest for whole tumors based on HR-T2WI and ADC maps. The least absolute shrinkage and selection operator (LASSO) was performed to select feature. The significantly difference was tested by the independent sample t-test and Mann-Whitney U test. The support vector machine (SVM) model was used to develop classification models. The correlation between features and T stage was assessed by Spearman's correlation analysis. Multivariate logistic regression analysis was performed to identify independent predictors of tumor invasion. The performance of classifiers was evaluated by the receiver operating characteristic (ROC) curves.
Results: The wavelet HHH NGTDM strength (RS = -0.364, P < 0.001) from HR-T2WI was an independent predictor of stage T3-4 tumors. The shape maximum 2D diameter column (RS = 0.431, P < 0.001), log σ = 5.0 mm 3D first-order maximum (RS = 0.276, P = 0.009), and log σ = 5.0 mm 3D first-order interquartile range (RS = -0.229, P = 0.032) from ADC maps were independent predictors. In training cohorts, the classification models from HR-T2WI, ADC maps and the combination of two achieved the area under the ROC curves (AUCs) of 0.877, 0.902 and 0.941, with the accuracy of 79.78%, 89.86% and 89.89%, respectively. In validation cohorts, the three models achieved AUCs of 0.845, 0.881 and 0.910, with the accuracy of 78.46%, 83.08% and 87.69%, respectively.
Conclusions: Texture analysis based on ADC maps shows more potential than HR-T2WI in identifying preoperative T stage in rectal carcinomas. The combined application of HR-T2WI and ADC maps may help to improve the accuracy of preoperative diagnosis of rectal cancer invasion.
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