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 2023
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 2023
- 1.1 Clinical Study of Puncture Technique in Single Division of the Trigeminal Ganglion Intumescentia
- 1.2 Dosimetric Assessment of Gadolinium-159 for Hepatic Radioembolization: Tomographic Images and Monte Carlo Simulation
- 1.3 The Cranial Capacity of the Saudi Population Measured Using 3D Computed Tomography Scans
- 1.4 The Tracheal System of the Common Wasp (Vespula Vulgaris) - a Micro-CT Study
- 1.5 Augmented Reality Presentation of the Extracranial Facial Nerve: An Innovation in Parotid Surgery
- 1.6 Magnetic Resonance Imaging in Naso-Oropharyngeal Carcinoma: Role of Texture Analysis in the Assessment of Response to Radiochemotherapy, a Preliminary Study
- 1.7 BabelBrain: An Open-Source Application for Prospective Modeling of Transcranial Focused Ultrasound for Neuromodulation Applications
- 1.8 Volumetric Analysis of the Sinus and Orbit in Silent Sinus Syndrome After Endoscopic Sinus Surgery
- 1.9 Safety and Efficacy of Thoracic Endovascular Aortic Repair for Acute Stanford Type B Aortic Dissection With Retrograde Type a Intramural Hematoma
- 1.10 The Traction Force of the Pulled Limb in Hip Arthroscopic Surgery Is Determined by Stiffness Coefficient Which Is Significantly Related to Muscle Volume
- 1.11 Three-Dimensional Assessment of Tongue Cancer Prognosis by Preoperative MRI
- 1.12 Multimodal Measurements of Levator Bowl Volume in Nulligravid Asymptomatic Women: Endovaginal Ultrasound Versus MRI
- 1.13 Pectoralis Muscle Area Measured at T4 Level Is Closely Associated With Adverse COVID-19 Outcomes in Hospitalized Patients
- 1.14 Precise Location of the Ventricular Catheter Tip in Ventriculoperitoneal Shunt Placement Guided by 3D Printed Individualized Guide
- 1.15 PIRET-A Platform for Treatment Planning in Electroporation-Based Therapies
- 1.16 Surgically Assisted Maxillary Expansion With or Without Pterygoid Disjunction Alters Maxillomandibular Positioning
- 1.17 ERCP 2.0: Biliary 3D-Reconstruction in Patients With Malignant Hilar Stricture
- 1.18 3D Printing Personalized Guide Plate in the Management of Recurrent Intramuscular Venous Malformations: A Single Center Experience
- 1.19 White Matter Hyperintensities: A Possible Link Between Sarcopenia and Cognitive Impairment in Patients With Mild to Moderate Alzheimer's Disease
- 1.20 CT Angiography Radiomics Combining Traditional Risk Factors to Predict Brain Arteriovenous Malformation Rupture: a Machine Learning, Multicenter Study
- 1.21 Real-Time Integration Between Microsoft HoloLens 2 and 3D Slicer With Demonstration in Pedicle Screw Placement Planning
- 1.22 Delirium After Traumatic Brain Injury: Prediction by Location and Size of Brain Lesion
- 1.23 Mitral Paravalvular Leak 3D Printing from 3D-Transesophageal Echocardiography
- 1.24 Prediction of Ki-67 Expression in Gastrointestinal Stromal Tumors Using Radiomics of Plain and Multiphase Contrast-Enhanced CT
- 1.25 Accuracy of Imaging Software for 3d Rendering of Tooth Structures, Usable in Clinical Settings
- 1.26 A Retrospective Three-Dimensional Study of the Mandibular Growth During Preoperative Orthodontics in Late Adolescent Patients With Skeletal Class III Malocclusion
- 1.27 Assessment of Variabilities in Lung-Contouring Methods on CBCT Preclinical Radiomics Outputs
- 1.28 A Training Tool for Clinicians in Segmenting Medical Images to Make 3D Models
- 1.29 3D Slicer Combined With Neuroendoscope in Treatment of a Distal Segment Aneurysm of the Anterior Choroidal Artery Complicated Intraventricular Hemorrhage: A Case Report and Literature Review
- 1.30 Application of Preoperative Multimodal Image Fusion Technique in Microvascular Decompression Surgery via Suboccipital Retrosigmoid Approach
- 1.31 An Interactive App with Multi-parametric MRI - Whole-Mount Histology Correlation for Enhanced Prostate MRI Training of Radiology Residents
- 1.32 3D Printed Guide Tube System for Acute Neuropixels Probe Recordings in Non-Human Primates
- 1.33 Diagnostic Value of 18F-FDG PET/CT-Based Radiomics Nomogram in Bone Marrow Involvement of Pediatric Neuroblastoma
- 1.34 Opportunistic Screening for Osteoporosis Using CT Scans of the Knee: A Pilot Study
- 1.35 Sustainable 3D Printing of Oral Films With Tunable Characteristics Using CMC-Based Inks From Durian Rind Wastes
- 1.36 An Automated Landmark Method to Describe Geometric Changes in the Human Mandible During Growth
- 1.37 Three-Dimensional Volume Rendering of Pelvic Floor Anatomy with Focus on Fibroids in Relation to the Lower Urogenital Tract Based on Cross-Sectional MRI Images
- 1.38 The First Endovascular Rat Glioma Model for Pre-Clinical Evaluation of Intra-Arterial Therapeutics
- 1.39 Muscle Magnetic Resonance Characterization of STIM1 Tubular Aggregate Myopathy Using Unsupervised Learning
- 1.40 Quantifying the Effect of an Endo-Vaginal Probe on Position of the Pelvic Floor Viscera and Muscles
- 1.41 Laser Interstitial Thermal Therapy in the Treatment of Brain Metastases: The Relationship Between Changes in Postoperative Magnetic Resonance Imaging Characteristics and Tumor Recurrence
- 1.42 Image Data and Computational Grids for Computing Brain Shift and Solving the Electrocorticography Forward Problem
- 1.43 ImFinite Element Analysis of a Healthy Knee Joint at Deep Squatting for the Study of Tibiofemoral and Patellofemoral Contact
- 1.44 A Comparison of Machine Learning Models for Survival Prediction of Patients with Glioma Using Radiomic Features from MRI Scans
- 1.45 Circular RNA hsa_circ_0000690 as a Potential Biomarker for Diagnosis and Prognosis of Intracranial Aneurysm: Closely Relating to the Volume of Hemorrhage
- 1.46 Can Quantitative Peritumoral CT Radiomics Features Predict the Prognosis of Patients With Non-Small Cell Lung Cancer? A Systematic Review
- 1.47 Three Dimensional Assessment of Radiographic Changes after Indirect Pulp Capping using Silver Diamine Fluoride with or without Potassium Iodide in Young Permanent Teeth (12-month RCT)
- 1.48 Cross-Sectional Reliability and Concurrent Validity of a Quantitative 2-Dimensional Ultrasound Image Analysis of Effusion and Synovial Hypertrophy in Knee Osteoarthritis
- 1.49 Patient-Specific Needle Guidance Templates Drilled Intraprocedurally for Image Guided Intervention: Feasibility Study in Swine
- 1.50 Automatic Landmark Identification in Cone-Beam Computed Tomography
- 1.51 Development and In-Silico and Ex-Vivo Validation of a Software for a Semi-Automated Segmentation of the Round Window Niche to Design a Patient Specific Implant to Treat Inner Ear Disorders
- 1.52 Design and Analysis of HSC-BPPV Diagnostic Maneuver Based on Virtual Simulation
- 1.53 The Simplified Tailor-Made Workflows for a 3D Slicer-Based Craniofacial Implant Design
- 1.54 Predicting Transient Ischemic Attack Risk in Patients With Mild Carotid Stenosis Using Machine Learning and CT Radiomics
- 1.55 Deep Learning Enabled Multi-Organ Segmentation of Mouse Embryos
- 1.56 Development and Validation of an 18FFDG-PET/CT Radiomic Model for Predicting Progression-Free Survival for Patients With Stage II - III Thoracic Esophageal Squamous Cell Carcinoma Who Are Treated With Definitive Chemoradiotherapy
- 1.57 Minimizing Magnetic Resonance Image Geometric Distortion at 7 Tesla for Frameless Presurgical Planning Using Skin-Adhered Fiducials
- 1.58 Acute Colonic Pseudo-Obstruction Secondary to Renal Calculus: A Case Report and Review of Pathophysiology
- 1.59 A Novel Stereotactic Aspiration Technique for Intracerebral Hemorrhage
- 1.60 Morphological Evaluation of the Normal and Hydrocephalic Third Ventricle on Cranial Magnetic Resonance Imaging in Children: A Retrospective Study
- 1.61 Henri IV of France's Larynx 3D Reconstitution
- 1.62 Development and External Validation of a Novel Nomogram to Predict Prostate Cancer in Biopsy-Naïve Patients With PSA <10 Ng/Ml and PI-RADS v2.1 = 3 Lesions
- 1.63 A Three-Dimensionally Printed Otological Model for Cholesteatoma Mastoidectomy Training
- 1.64 Development of a Navigable 3D Virtual Model of Temporal Bone Anatomy
- 1.65 Maxillary Antral Pseudocyst Drift after Osteotome Sinus Floor Elevation with Simultaneous Implant Placement: A Case Report and Literature Review
- 1.66 Radiomic Analysis Based on Magnetic Resonance Imaging for Predicting PD-L2 Expression in Hepatocellular Carcinoma
- 1.67 Correlation Between Unilateral Internal Carotid Artery Stenosis and Asymmetric Distribution of Enlarged Perivascular Spaces in Patients With Acute Cerebral Infarction
- 1.68 Radiomics to Predict the Mortality of Patients With Rheumatoid Arthritis-Associated Interstitial Lung Disease: A Proof-of-Concept Study
- 1.69 Evaluation of the Prognosis of Acute Subdural Hematoma According to the Density Differences Between Gray and White Matter
- 1.70 The Knosp Criteria Revisited: 3-Dimensional Volumetric Analysis as a Predictive Tool for Extent of Resection in Complex Endoscopic Pituitary Surgery
- 1.71 Differentiation of Lung Metastases Originated From Different Primary Tumors Using Radiomics Features Based on CT Imaging
- 1.72 MRI Radiomic Features of Peritumoral Edema May Predict the Recurrence Sites of Glioblastoma Multiforme
- 1.73 Clinical Study on Application of 3D Slicer Software Assisted Domestic Frameless Stereotactic Robot in Biopsy of Intracranial Lesions
- 1.74 Liver Cirrhosis and Tumor Location Can Affect the Range of Intrahepatic Microwave Ablation Zone
- 1.75 A Magnetic Resonance Imaging Based Radiomics Model to Predict Mitosis Cycles in Intracranial Meningioma
- 1.76 Advantages of a Training Course for Surgical Planning in Virtual Reality for Oral and Maxillofacial Surgery: Crossover Study
- 1.77 Lesion Size and Long-Term Cognitive Outcome After Pediatric Stroke: A Comparison Between Two Techniques to Assess Lesion Size
- 1.78 Association Between Emphysema and Other Pulmonary Computed Tomography Patterns in COVID-19 Pneumonia
- 1.79 A High-Resolution Pediatric Female Whole-Body Numerical Model With Comparison to a Male Model
- 1.80 Anatomical Morphology and Related Angles of Foramen Ovale: A Three-dimensional Computed Tomography Reconstruction
Clinical Study of Puncture Technique in Single Division of the Trigeminal Ganglion Intumescentia
Authors: Zhang L, Guo Y, Xu J, He Y, Qi Z, Chen H, Zhang H.
Institution: Department of Neurosurgery, Jianhu Hospital Affiliated to Nantong University, Yancheng, China.
Abstract: Objective: We explored the feasibility of single-division puncture in the ophthalmic division, maxillary division, and mandibular division of the trigeminal ganglion intumescentia (TGI) and the feasibility of radiofrequency treatment of trigeminal neuralgia.
Methods: According to the previous anatomical image studies, 3D Slicer software was used to analyze the CT images of the patients. The trigeminal ganglion fossa (TGF) was used as the imaging sign. TGI was identified in the sagittal plane along the fiber. The puncture path starts from the TGI center-foramen ovale line, extending outward to the epidermis as the needle insertion point, and extending inward to the division boundary. For lateral puncture, which is blocked by the mandible, the positions of closed mouth, open mouth, and over-open mouth were used. Multiple targets were generated using straight electrodes and curved electrodes to achieve full coverage of TGI. According to the preoperative design, general anesthesia surgery was performed. Xper CT was used for imaging, and the puncture was guided by Xper Guide. Radiofrequency treatment of TGI was conducted.
Results: In total, 45 patients with trigeminal neuralgia underwent 50 single-division TGI punctures. The procedure was smooth and the compliance with the design was good. Continuous radiofrequency (CRF) was performed, the VAS scores were 25 times at 70°C, 19 times at 65°C, two times at 60°C, and two times at 50°C (both in the ophthalmic division). Pulsed radiofrequency (PRF) was conducted two times. Within 24 h after the procedure, the VAS scores were all 0. From 1 to 7 days after the procedure, pain recurrence was found in three cases, of whom two cases received pulsed radiofrequency treatment. Patients were followed up for 1-24 months and there were no recurrence. After continuous radiofrequency at 65-70°C, the moderate tactile loss was observed, and nearly half of the patients had food residues on the surgical side after 6 months. After continuous radiofrequency at 60°C, there was mild tactile loss and no food residue. The tactile sensation was slightly decreased after continuous radiofrequency at 50°C, and the tactile sensation was normal the next day.
Conclusion: Trigeminal ganglion intumescentia single-division radiofrequency is effective and feasible for the treatment of trigeminal neuralgia.
Dosimetric Assessment of Gadolinium-159 for Hepatic Radioembolization: Tomographic Images and Monte Carlo Simulation
Authors: Musa AS, Abdul Hadi MFR, Hashikin NAA, Ashour NI, Ying CK.
Institution: School of Physics, Universiti Sains Malaysia, Penang, Malaysia.
Abstract: A common therapeutic radionuclide used in hepatic radioembolization is yttrium-90 (90Y). However, the absence of gamma emissions makes it difficult to verify the post-treatment distribution of 90Y microspheres. Gadolinium-159 (159Gd) has physical properties that are suitable for therapy and post-treatment imaging in hepatic radioembolization procedures. The current study is innovative for conducting a dosimetric investigation of the use of 159Gd in hepatic radioembolization by simulating tomographic images using the Geant4 application for tomographic emission (GATE) Monte Carlo (MC) simulation. For registration and segmentation, tomographic images of five patients with hepatocellular carcinoma (HCC) who had undergone transarterial radioembolization (TARE) therapy were processed using a 3D Slicer. The tomographic images with 159Gd and 90Y separately were simulated using the GATE MC Package. The output of simulation (dose image) was uploaded to 3D Slicer to compute the absorbed dose for each organ of interests. 159Gd were able to provide a recommended dose of 120 Gy to the tumour, with normal liver and lungs absorbed doses close to that of 90Y and less than the respective maximum permitted doses of 70 Gy and 30 Gy, respectively. Compared to 90Y, 159Gd requires higher administered activity approximately 4.92 times to achieve a tumour dose of 120 Gy. Thus; this research gives new insights into the use of 159Gd as a theranostic radioisotope, with the potential to be used as a90Y alternative for liver radioembolization.
The Cranial Capacity of the Saudi Population Measured Using 3D Computed Tomography Scans
Authors: Alshamrani KA.
Institution: Department of Radiological sciences, Faculty of Applied Medical Science, and from Health Research Centre, Najran University, Najran, Kingdom of Saudi Arabia.
Abstract: Objectives: To measure the cranial capacity of members of the Saudi adult population across ages and genders.
Methods: This was a retrospective cross-sectional study that used 488 Computed Tomography (CT) scans of heads (of which 275 males) to measure cranial volume. The CT slices 0.625 mm thick were uploaded using the freely available 3D Slicer software, which then reconstructed the images and built a 3D module.
Results: The mean (±SD) cranial capacity of the males was 1481.6 (±110) cm3 (range: 1241-1723 cm3), whereas the cranial capacity of the females was 1375.4 (±104) cm3 (range: 1203-1678 cm3). This study showed that the males had a mean cranial capacity that was 7% greater than that of the females in this study. The average cranial capacity of the males between the ages of 31 and 40 years was statistically significantly larger to that of the males aged 61-80 (p<0.05).
Conclusion: This study demonstrated that the average cranial capacity of the males was larger than that of the females. These study results can help to determine the normal cranial capacity of adults in Saudi Arabia. Further work should be carried out to aid in establishing reference data for the Saudi population.
The Tracheal System of the Common Wasp (Vespula Vulgaris) - a Micro-CT Study
Authors: Bell GD, Corps N, Mortimer D, Gretton S, Bury N, Connett GJ.
Institution: School of (EAST) Engineering, Arts, Science and Technology, University of Suffolk, James Hehir Building, UK.
Abstract: X-ray micro-CT has been used to study the tracheal system of Pre and Post hibernation Queen wasps (Vespula vulgaris) and their workers. We have compared our findings in wasps with Snodgrass's description of the tracheal system of the honeybee as characterised by anatomical dissection. Our images, whilst broadly similar, identify the tracheal system as being considerably more complex than previously suggested. One of the 30 wasps imaged had a markedly different, previously undescribed tracheal system. Since completing this study, a large micro-CT study from the American Museum of Natural History (AMNH) has been published. This used different software, 3D Slicer and analysed 16bit digital data. We have compared our methods with that described in the AMNH publication, adopted their suggested nomenclature and have made recommendations for future studies.
Augmented Reality Presentation of the Extracranial Facial Nerve: An Innovation in Parotid Surgery
Authors: Saadya A, Chegini S, Morley S, McGurk M.
Institution: University College London Hospital, UK.
Abstract: Surgeons used to be unaware of the facial nerve's position during parotid surgery. Now, with special magnetic resonance imaging (MRI) sequences, it can be located and converted into a 3D model displayed on an augmented reality (AR) device for surgeons to study and manipulate. This study explores the accuracy and usefulness of the technique for the treatment of benign and malignant parotid tumours. A total of 20 patients with parotid tumours had 3-Tesla MRI scans, and their anatomical structures were segmented using 3D Slicer software. The structures were imported into a Microsoft HoloLens 2® device, displayed in 3D, and shown to the patient for consent. Intraoperative video recording was used to record the position of the facial nerve in relation to the tumour. The predicted path of the nerve taken from the 3D model was combined with surgical observation and video recording in all cases. The imaging proved to have application in both benign and malignant disease. It also improved the process of informed patient consent. Three-dimensional MRI imaging of the facial nerve within the parotid gland and its display in a 3D model is an innovative technique for parotid surgery. Surgeons can now see the nerve's position and tailor their approach to each patient's tumour, providing personalised care. The technique eliminates the surgeon's blind spot and is a significant advantage in parotid surgery.
Magnetic Resonance Imaging in Naso-Oropharyngeal Carcinoma: Role of Texture Analysis in the Assessment of Response to Radiochemotherapy, a Preliminary Study
Publication: Radiol Med. 2023 Jul;128(7):839-52. PMID: 37336860 | PDF
Authors: Bicci E, Nardi C, Calamandrei L, Barcali E, Pietragalla M, Calistri L, Desideri I, Mungai F, Bonasera L, Miele V.
Institution: Department of Experimental and Clinical Biomedical Sciences, Radiodiagnostic Unit #2, University of Florence, Florence, Italy.
Abstract: Objective: Identifying MRI texture parameters able to distinguish inflammation, fibrosis, and residual cancer in patients with naso-oropharynx carcinoma after radiochemotherapy (RT-CHT).
Material and methods: In this single-centre, observational, retrospective study, texture analysis was performed on ADC maps and post-gadolinium T1 images of patients with histological diagnosis of naso-oropharyngeal carcinoma treated with RT-CHT. An initial cohort of 99 patients was selected; 57 of them were later excluded. The final cohort of 42 patients was divided into 3 groups (inflammation, fibrosis, and residual cancer) according to MRI, 18F-FDG-PET/CT performed 3-4 months after RT-CHT, and biopsy. Pre-RT-CHT lesions and the corresponding anatomic area post-RT-CHT were segmented with 3D Slicer software from which 107 textural features were derived. T-Student and Wilcoxon signed-rank tests were performed, and features with p-value < 0.01 were considered statistically significant. Cut-off values-obtained by ROC curves-to discriminate post-RT-CHT non-tumoural changes from residual cancer were calculated for the parameters statistically associated to the diseased status at follow-up.
Results: Two features-Energy and Grey Level Non-Uniformity-were statistically significant on T1 images in the comparison between 'positive' (residual cancer) and 'negative' patients (inflammation and fibrosis). Energy was also found to be statistically significant in both patients with fibrosis and residual cancer. Grey Level Non-Uniformity was significant in the differentiation between residual cancer and inflammation. Five features were statistically significant on ADC maps in the differentiation between 'positive' and 'negative' patients. The reduction in values of such features between pre- and post-RT-CHT was correlated with a good response to therapy.
Conclusions: Texture analysis on post-gadolinium T1 images and ADC maps can differentiate residual cancer from fibrosis and inflammation in early follow-up of naso-oropharyngeal carcinoma treated with RT-CHT.
BabelBrain: An Open-Source Application for Prospective Modeling of Transcranial Focused Ultrasound for Neuromodulation Applications
Authors: Pichardo S.
Institution: Department of Radiology, University of Calgary, Calgary, Canada.
Abstract: BabelBrain is an open-source standalone graphic-user-interface application designed for studies of neuromodulation using transcranial-focused ultrasound (FUS). It calculates the transmitted acoustic field in the brain tissue, taking into account the distortion effects caused by the skull barrier. The simulation is prepared using scans from magnetic resonance imaging (MRI) and, if available, computed tomography (CT) and zero-echo time MRI scans. It also calculates the thermal effects based on a given ultrasound regime, such as the total duration of exposure, the duty cycle, and acoustic intensity. The tool is designed to work in tandem with neuronavigation and visualization software, such as 3D Slicer. It uses image processing to prepare domains for ultrasound simulation and uses the BabelViscoFDTD library for transcranial modeling calculations. BabelBrain supports multiple GPU backends, including Metal, OpenCL, and CUDA, and works on all major operating systems including Linux, macOS, and Windows. This tool is particularly optimized for Apple ARM64 systems, which are common in brain imaging research. The article presents the modeling pipeline used in BabelBrain and a numerical study where different methods of acoustic properties mapping were tested to select the best method that can reproduce the transcranial pressure transmission efficiency reported in the literature.
Volumetric Analysis of the Sinus and Orbit in Silent Sinus Syndrome After Endoscopic Sinus Surgery
Authors: Amin D, Chitguppi C, Xu V, Haghshenas C, Gorniak R, Rabinowitz M, Toskala E, Rosen M, Nyquist G.
Institution: Department of Otolaryngology-Head & Neck Surgery, Thomas Jefferson University, Philadelphia, PA, USA.
Abstract: Objective: The term "silent sinus syndrome" (SSS) describes spontaneous enophthalmos secondary to subclinical maxillary sinus atelectasis. Debate remains on whether treatment with endoscopic maxillary antrostomy alone is adequate in reversing atelectasis and globe displacement. This study aims to determine the degree of volume change of the diseased sinus and orbit as well as the change in orbital height in patients treated with endoscopic antrostomy without orbital floor augmentation.
Study design: Retrospective review with image analysis.
Setting: Single tertiary care institution.
Methods: Three-dimensional (3D) analysis of computed tomographic imaging data was performed using 3D Slicer. 3D models of the maxillary sinus and orbit of the diseased and normal sides were created, and volume measurements were calculated using the segmentation program.
Results: Thirteen patients with SSS who underwent endoscopic sinus surgery (ESS) and had follow-up computed tomographic imaging were analyzed. After endoscopic antrostomy, the mean volume of the diseased maxillary sinus significantly increased by 9.82%, from 6.37 to 7.00 cm3 (p = .0302). There was no significant change in mean orbital volume; however, the mean orbital height decreased by 5.67%, from 38.09 to 35.93 mm from pretreatment to posttreatment samples (p = .0101). All patients had resolution of clinical or radiographic enophthalmos and orbital displacement with ESS alone.
Conclusion: Endoscopic maxillary antrostomy alone in the treatment of SSS significantly increased maxillary sinus volume and decreased diseased orbital height. These changes were associated with clinical and radiographic improvement in globe displacement. These findings support performing ESS alone, reserving orbital augmentation for patients who do not exhibit adequate clinical improvement.
Safety and Efficacy of Thoracic Endovascular Aortic Repair for Acute Stanford Type B Aortic Dissection With Retrograde Type a Intramural Hematoma
Publication: J Vasc Surg. 2023 Jul;78(1):61-69.e4. PMID: 36921645 | PDF
Authors: Wang J, Li M, Li J, He H, Zhou Y, Li X, Li Q, Gu F, Ye Z, Dardik A, Shu C.
Institution: Department of Vascular Surgery, Second Xiangya Hospital, Central South University, Changsha, China; Institute of Vascular Diseases, Central South University, Changsha, China.
Abstract: Objective: The aim of this study was to evaluate safety and efficacy of thoracic endovascular aortic repair (TEVAR) for acute Stanford type B aortic dissection (TBAD) with retrograde type A intramural hematoma (TAIMH).
Methods: Patients with acute TBAD with retrograde TAIMH treated with TEVAR between January 1, 2014, to March 31, 2022, were retrospectively reviewed. Aortic diameter and distance were measured using the 3D Slicer image computing platform. Patients' characteristics, procedural, in-hospital and follow-up data, and aortic remodeling were analyzed.
Results: Fifty-two patients (average age, 52.6 years; 42 males [80.8%]) were included. The median interval from symptom onset to TEVAR was 11 days (interquartile range, 7.0-16.8 days). The maximal diameter of the ascending aorta (AA) was <50 mm, and the hematoma thickness in the AA was ≤10 mm in all patients. Both the in-hospital and 30-day mortality rates were 0%. The 30-day complication rate was 11.5%. The overall cumulative survival rates were 100% at 1 year, 97.1% at 3 years, and 92.6% at 5 years. Four of 52 patients (7.7%) developed retrograde type A aortic dissection at 10 days to 4 months postoperatively, and one of 52 patients (1.9%) developed an isolated AA dissection 4 months postoperatively; these five patients were treated and alive at late follow-up in March 2022. The rates of cumulative freedom from thoracic aortic re-intervention were 93.7% at 1 year and 90.7% at 5 years. Positive AA remodeling was observed in 92.3% (48/52) of patients during follow-up. The maximal diameter of AA (mean ± standard error of mean) at admission was 42.7 ± 0.8 mm, which decreased to 39.5 ± 0.9 mm at last follow-up. The maximal AA hematoma thickness at admission was 7.6 ± 0.3 mm, which reduced to 2.2 ± 0.9 mm at last follow-up.
Conclusions: For selected patients of acute Stanford TBAD with retrograde TAIMH, endovascular repair may be a safe, effective, and durable alternative treatment, if the maximum diameter of the AA is <50 mm and the intramural hematoma thickness in the AA is ≤10 mm.
The Traction Force of the Pulled Limb in Hip Arthroscopic Surgery Is Determined by Stiffness Coefficient Which Is Significantly Related to Muscle Volume
Authors: Yin Y, Xue S, Zhang X, Yang G, Xu Y, Wang J, Huang H.
Institution: Department of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Institute of Sports Medicine of Peking University, Beijing, People's Republic of China.
Abstract: Purpose: To verify the relationship between muscle volume, lateral centre-edge angle (LCEA), alpha angle (AA), body mass index (BMI) and Beighton score with stiffness coefficient (SC). To analyse the difference of traction force at different physical states of hip joint capsule.
Methods: Thirty-six patients who underwent hip arthroscopy operation were included. The volumes of some related muscles were measured in MRI images by 3D Slicer. We recorded and tested differences in traction force of five joint capsule physical states, including before (State 1) and after joint capsule puncture (State 2), after the establishment of anterolateral and mid-anterior approaches (State 3) and after incision of the joint capsule through these two approaches (States 4, 5). The correlation between muscle volume, BMI, LCEA, AA and SC was verified by Spearman test. Poisson regression was used to explain confounding variables.
Results: The average force at State 1 was 531.8 N. There were significant differences in traction force between these five states (p < 0.001). There was a significant positive correlation between muscle volumes and SC (p < 0.001). BMI had no correlation with SC (n.s.). The preoperative LCEA of the affected side was correlated with SC (p = 0.043). AA and SC were not correlated (n.s.).
Conclusion: The physical states of the hip joint capsule affected traction force. Muscle volume rather than BMI is an ideal index to estimate preoperative traction force. LCEA affected traction force, whilst AA and Beighton score did not. Measuring the muscle volume can help estimate the most suitable traction force for the patient.
Three-Dimensional Assessment of Tongue Cancer Prognosis by Preoperative MRI
Publication: Oral Dis. 2023 Jul;29(5):2006-2011. PMID: 35426211
Authors: Li C, Zhu L, Guo Y, Ji T, Ren Z.
Institution: Department of Oral and Maxillofacial Head and Neck Oncology, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Abstract: Purpose: To obtain the relative volume by measuring the tongue volume and the lesion volume, and further explore its relationship with the prognosis of patients, hoping to supplement the TNM staging with a new index.
Methods: ITK-SANP software was used to outline the patients' MRI. After MRI reconstruction and measurement, 3D Slicer software was used to estimate tumor volume.
Results: A total of 64 patients with tongue cancer who met the inclusion criteria were included in the study. The estimated tumor volume after MRI reconstruction revealed a significant and robust correlation with tumor stage (p < 0.05, Rs = 0.6207) and a substantial and medium correlation with early lymph node metastasis (p < 0.05, Rs = 0.4873).
Conclusions: We classified tongue cancer into three grades based on tumor volume (Stage I, tumors smaller than 1500 mm³; Stage II, tumors 1500-9000 mm³; and Stage III, tumors larger than 9000 mm³), and such grading could be used as a reference for tumor staging, lymph node metastasis, and patient prognosis to a certain extent.
Multimodal Measurements of Levator Bowl Volume in Nulligravid Asymptomatic Women: Endovaginal Ultrasound Versus MRI
Authors: Chill HH, Martin LC, Abramowitch SD, Rostaminia G.
Institution: Female Pelvic Medicine and Reconstructive Surgery (FPMRS), Division of Urogynecology, University of Chicago, Northshore University HealthSystem, Skokie, IL, USA.
Abstract: Introduction and hypothesis: Measurements of levator bowl volume using advanced imaging, may be predictive of pelvic floor muscle function. The aim of this study was to compare the volume of the levator bowl using both magnetic resonance imaging (MRI) and endovaginal ultrasound (EVU) of healthy asymptomatic women.
Methods: All participants underwent a comprehensive interview including completion of the Pelvic Floor Distress Inventory Questionnaire-20 questionnaire, pelvic examination with a pelvic organ prolapse quantification evaluation, MRI, and EVU. The pelvic floor was segmented using 3D Slicer and the MRI segmentations were trimmed using two methods: soft-tissue landmarks and the field of view (FOV) of the ultrasound volume. The levator bowl volume of the 3D segmented shapes was measured using Blender's 3D printing toolkit. Normality was tested using the Shapiro-Wilks test and comparisons were made using self-paired t tests.
Results: The final analysis included 19 patients. Levator bowl volume measured via MRI was larger than that measured in EVU (46.1 ± 7.9 cm3 vs 27.4 ± 5.9 cm3, p<0.001). Reducing the FOV of the MRI to that of EVU caused the MRI volume to be much closer to the EVU volume (35.5 ± 3.3 cm3 vs 27.4 ± 5.9 cm3, p<0.001); however, it remained significantly larger.
Conclusion: Levator bowl volume measured using MRI was larger than that measured using EVU no matter the method of delineation of the levator muscles. Although EVU is safe, cheap, and easy to perform, it captures a smaller volume of levator bowel than MRI.
Pectoralis Muscle Area Measured at T4 Level Is Closely Associated With Adverse COVID-19 Outcomes in Hospitalized Patients
Institution: Istanbul Medeniyet University, Goztepe Prof Dr Suleyman Yalcin City Hospital, Radiology, Istanbul, Turkey.
Abstract: Objectives: Skeletal muscle area (SMA) at T4 level on chest computed tomography (CT) is a newly available method that can be used as a surrogate sarcopenia marker. The objective of this study is to evaluate association of SMA with adverse COVID-19 outcomes in hospitalized patients.
Methods: Hospitalized COVID-19 patients were prospectively recorded in a database containing age, gender, date of admission, date of outcome (discharge, mortality, presence of intensive care unit (ICU) stay, additional coding information (comorbidities, superimposed conditions). Admission CT-scans were retrospectively evaluated for segmentation (bilateral pectoralis major/minor, erector spinae, levator scapulae, rhomboideus minor and major and transversospinalis muscles) and SMA calculation using 3D Slicer software.
Results: 167 cases were evaluated (68 male, 72 female, 140 survived, 27 dead). Muscle area was lower in patients with ICU stay (p=0.023, p=0.018, p=0.008) and mortality outcome (p=0.004, p=0.007, p=0.002) for pectoralis, back and SMA. In multivariate Cox-regression analysis, hazard ratio (HR) value for the pectoralis muscle area value below 2800 mm2 was found to be 3.138(95% CI: 1.171-8.413) for mortality and 2.361(95% CI: 1.012-5.505) for ICU.
Conclusions: Pectoralis muscle area measured at T4 level with 3-D slicer was closely associated with adverse outcomes (mortality, ICU stay) in hospitalized COVID-19 patients. Since early treatment methods for COVID-19 are being evaluated, this method may be a useful adjunct to clinical decision making in regard to prioritization.
Precise Location of the Ventricular Catheter Tip in Ventriculoperitoneal Shunt Placement Guided by 3D Printed Individualized Guide
Institution: Department of Neurosurgery, Tangdu hospital, Air Force Medical University, Shaanxi, China.
Abstract: Objective: Improper placement of the ventricular catheter tip is the most common cause of shunting disorders after ventriculoperitoneal shunt (VPS) placement surgery. Here, through two illustrative cases, we described a novel method of precise ventricular catheter tip location.
Methods: 3D Slicer software was used to define the ventricle puncture path and determine the ventricle catheter tip location preoperatively, and the 3D individualized guide model was printed.
Results: The ventricular puncture was performed under the guidance of the 3D guide to achieve precise ventricle catheter tip location intraoperatively.
Conclusions: This technique is safe, simple, efficient and cost-effective, which facilitates its clinical implementation and promotion.
PIRET-A Platform for Treatment Planning in Electroporation-Based Therapies
Institution: BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain.
Abstract: Tissue electroporation is the basis of several therapies. Electroporation is performed by briefly exposing tissues to high electric fields. It is generally accepted that electroporation is effective where an electric field magnitude threshold is overreached. However, it is difficult to preoperatively estimate the field distribution because it is highly dependent on anatomy and treatment parameters.
Objective: We developed PIRET, a platform to predict the treatment volume in electroporation-based therapies.
Methods: The platform seamlessly integrates tools to build patient-specific models where the electric field is simulated to predict the treatment volume. Patient anatomy is segmented from medical images and 3D reconstruction aids in placing the electrodes and setting up treatment parameters.
Results: Four canine patients that had been treated with high-frequency irreversible electroporation were retrospectively planned with PIRET and with a workflow commonly used in previous studies, which uses different general-purpose segmentation, 3D Slicer and modeling software (3Matic and COMSOL Multiphysics). PIRET outperformed the other workflow by 65 minutes (× 1.7 faster), thanks to the improved user experience during treatment setup and model building. Both approaches computed similarly accurate electric field distributions, with average Dice scores higher than 0.93.
Conclusion: A platform which integrates all the required tools for electroporation treatment planning is presented. Treatment plan can be performed rapidly with minimal user interaction in a stand-alone platform.
Significance: This platform is, to the best of our knowledge, the most complete software for treatment planning of irreversible electroporation. It can potentially be used for other electroporation applications.
Surgically Assisted Maxillary Expansion With or Without Pterygoid Disjunction Alters Maxillomandibular Positioning
Institution: Department of Oral and Maxillofacial Surgery, Federal University of Ceará Campus Sobral, Brazil.
Abstract: Purpose: This study aimed to analyze alterations in mandibular positioning after surgically assisted maxillary expansion (SARME) with and without pterygoid disjunction (PD).
Methods: Cone-beam computed tomography scans of 24 healthy individuals (18-45 years old) with transverse deficiency, superior to 5 mm, underwent SARME with or without PD. The aspects prospectively assessed were (1) alignment and position of the head (ITK-Snap and 3D Slicer software); (2) McNamara's and Steiner-Tweed-Wits' cephalometric analysis (Dolphin Imaging®); and (3) colorimetric evaluation based on 3D correspondence analysis (3D Slicer software).
Results: A decrease in 1-NA and 1-SN angles as well as an increased occlusal plane in both groups was observed. Superior-inferior and anteroposterior spatial displacements of the chin were statistically significant in the PD group. Altered colorimetric patterns were also observed in the PD group.
Conclusions: This study found more evident tooth inclination in the group without PD; mandibular alterations were more evident in the PD group. Further studies with 3D analysis are strongly recommended for more comprehensive results.
ERCP 2.0: Biliary 3D-Reconstruction in Patients With Malignant Hilar Stricture
Authors: Becq A, Szewczyk J, Salin G, Chartier M, Chaput U, Leenhardt R, Dray X, Arrive L, Camus M.
Institution: Department of Gastroenterology, Henri-Mondor University Hospital, AP-HP, EA 7375, Université Paris Est Créteil, France.
Abstract: Background: Endoscopic retrograde cholangiopancreatography (ERCP) for malignant hilar strictures is challenging. The correlation between Magnetic resonance cholangiopancreatography (MRCP) and per ERCP 2D fluoroscopic images is not obvious. The aim of this study was to evaluate the feasibility and potential usefulness of MRCP-based handmade biliary 3D reconstruction in this setting.
Methods: Methods Patients who underwent MRCP followed by ERCP for biliary drainage of a malignant hilar stricture at our institution between 2018 and 2020 were reviewed. A handmade 3D segmentation using 3D Slicer (Kitware, France) was fashioned and reviewed with an expert radiologist. The primary outcome was the feasibility of biliary segmentation.
Results: A total of 16 patients were included. The mean age was 70.1 (+/- 8.6) years-old and 68.8% had hilar cholangiocarcinoma. Handmade segmentation was successful in all cases. The agreement between the MRCP interpretation and the 3D reconstruction was 37.5%, as per the Bismuth classification. 3D reconstruction available prior to ERCP could have helped guide for better stent placement in 11 cases (68.8%).
Conclusions: MRCP-based biliary 3D segmentation-reconstruction, in patients with malignant hilar stricture is feasible and seems to provide a better anatomical understanding compared to MRCP and could help improve endoscopic management.
3D Printing Personalized Guide Plate in the Management of Recurrent Intramuscular Venous Malformations: A Single Center Experience
Publication: Phlebology. 2023 Jun;38(5):307-314. PMID: 36967547
Institution: Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, China.
Abstract: Objective: This study aimed to investigate the feasibility and effectiveness of 3D printing personalized guide plate in the management of recurrent intramuscular venous malformations (IVM).
Methods: Fifteen patients with recurrent IVM were retrospectively assessed. 3D Slicer software was used to extract and reconstruct the imaging data from CT and/or MRI to highlight the morphology, size, and puncture depth of the lesion. With the guidance of personalized plate, complete excision of the IVM was adopted along the pre-marked (methylene blue, MB) margin.
Results: Personalized guide plate matched involved extremity well, and MB-puncture approach was consistent with preoperative design. All IVMs were removed radically in one single session. Complete pain relief was obtained in all cases postoperatively.
Conclusion: The application of 3D printing guide plate can be safe, effective, and reliable to confirming the precise margin of IVM, renders a promising technique with a high practical value in resection of recurrent lesion.
White Matter Hyperintensities: A Possible Link Between Sarcopenia and Cognitive Impairment in Patients With Mild to Moderate Alzheimer's Disease
Publication: Eur Geriatr Med. 2023 Jun 18. PMID: 37330930
Authors: Weng X, Liu S, Li M, Zhang Y, Zhu J, Liu C, Hu H.
Institution: Department of Neurology, The Second Affiliated Hospital of Soochow University, Jiangsu, China.
Abstract: Purpose: Alzheimer's disease (AD) has been reported to be associated with sarcopenia. White matter hyperintensities (WMH) are common in AD patients. However, the effect of WMH on sarcopenia in AD remains unclear. We hence aimed to investigate the possible association between regional WMH volumes and sarcopenic parameters in AD.
Methods: 57 mild to moderate AD patients and 22 normal controls (NC) were enrolled. Sarcopenic parameters were assessed, including appendicular skeletal mass index (ASMI), grip strength, 5-times sit-to-stand (5-STS) time, and gait speed. The volumes of periventricular hyperintensities (PVH) and deep white matter hyperintensities (DWMH) were quantified using 3D Slicer software.
Results: AD subjects exhibited a lower ASMI, a slower gait speed, an increased 5-STS time, and larger volumes of PVH and DWMH than those in the NC group. In AD subjects, total WMH and PVH volumes were related to cognitive impairment, particularly executive function decline. Moreover, total WMH volume and PVH volume were negatively correlated with gait speed across various clinical stages of AD. Multiple linear regression analysis showed that PVH volume was independently associated with 5-STS time and gait speed, whereas DWMH volume was only independently associated with gait speed.
Conclusion: WMH volume was associated with cognitive decline and various sarcopenic parameters. It thereby suggested that WMH may serve as the connection between sarcopenia and cognitive dysfunction in AD. Further studies are needed to confirm these findings and to determine whether sarcopenia interventions reduce WMH volume and improve cognitive function in AD.
CT Angiography Radiomics Combining Traditional Risk Factors to Predict Brain Arteriovenous Malformation Rupture: a Machine Learning, Multicenter Study
Publication: Transl Stroke Res. 2023 Jun 13. PMID: 37311939
Authors: Zhang S, Wang J, Sun S, Zhang Q, Zhai Y, Wang X, Ge P, Shi Z, Zhang D.
Institution: Department of Neurosurgery, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.
Abstract: This study aimed to develop a machine learning model for predicting brain arteriovenous malformation (bAVM) rupture using a combination of traditional risk factors and radiomics features. This multicenter retrospective study enrolled 586 patients with unruptured bAVMs from 2010 to 2020. All patients were grouped into the hemorrhage (n = 368) and non-hemorrhage (n = 218) groups. The bAVM nidus were segmented on CT angiography images using 3D Slicer software, and radiomic features were extracted using Pyradiomics. The dataset included a training set and an independent testing set. The machine learning model was developed on the training set and validated on the testing set by merging numerous base estimators and a final estimator based on the stacking method. The area under the receiver operating characteristic (ROC) curve, precision, and the f1 score were evaluated to determine the performance of the model. A total of 1790 radiomics features and 8 traditional risk factors were contained in the original dataset, and 241 features remained for model training after L1 regularization filtering. The base estimator of the ensemble model was Logistic Regression, whereas the final estimator was Random Forest. In the training set, the area under the ROC curve of the model was 0.982 (0.967-0.996) and 0.893 (0.826-0.960) in the testing set. This study indicated that radiomics features are a valuable addition to traditional risk factors for predicting bAVM rupture. In the meantime, ensemble learning can effectively improve the performance of a prediction model.
Real-Time Integration Between Microsoft HoloLens 2 and 3D Slicer With Demonstration in Pedicle Screw Placement Planning
Authors: Pose-Díez-de-la-Lastra A, Ungi T, Morton D, Fichtinger G, Pascau J.
Institution: Departamento de Bioingeniería, Universidad Carlos III de Madrid, Spain.
Abstract: Purpose: Up to date, there has been a lack of software infrastructure to connect 3D Slicer to any augmented reality (AR) device. This work describes a novel connection approach using Microsoft HoloLens 2 and OpenIGTLink, with a demonstration in pedicle screw placement planning.
Methods: We developed an AR application in Unity that is wirelessly rendered onto Microsoft HoloLens 2 using Holographic Remoting. Simultaneously, Unity connects to 3D Slicer using the OpenIGTLink communication protocol. Geometrical transform and image messages are transferred between both platforms in real time. Through the AR glasses, a user visualizes a patient's computed tomography overlaid onto virtual 3D models showing anatomical structures. We technically evaluated the system by measuring message transference latency between the platforms. Its functionality was assessed in pedicle screw placement planning. Six volunteers planned pedicle screws' position and orientation with the AR system and on a 2D desktop planner. We compared the placement accuracy of each screw with both methods. Finally, we administered a questionnaire to all participants to assess their experience with the AR system.
Results: The latency in message exchange is sufficiently low to enable real-time communication between the platforms. The AR method was non-inferior to the 2D desktop planner, with a mean error of 2.1 ± 1.4 mm. Moreover, 98% of the screw placements performed with the AR system were successful, according to the Gertzbein-Robbins scale. The average questionnaire outcomes were 4.5/5.
Conclusions: Real-time communication between Microsoft HoloLens 2 and 3D Slicer is feasible and supports accurate planning for pedicle screw placement.
Delirium After Traumatic Brain Injury: Prediction by Location and Size of Brain Lesion
Publication: Ann Rehabil Med. 2023 Jun;47(3):214-21. PMID: 37317796 | PDF
Authors: Han SJ, Suh JH, Lee JY, Kim SJ.
Institution: Department of Rehabilitation Medicine, College of Medicine, Ewha Womans University, Seoul, Korea.
Abstract: Objective: To examine (1) the location of brain lesion that would predict post-traumatic delirium and (2) the association between volume of brain lesion and occurrence of delirium in patients with traumatic brain injury (TBI).
Methods: A retrospective study was conducted by reviewing medical records of 68 TBI patients, categorized into two groups: the delirious group (n=38) and non-delirious group (n=30). The location and volume of TBI were investigated with the 3D Slicer software.
Results: The TBI region in the delirious group mainly involved the frontal or temporal lobe (p=0.038). All 36 delirious patients had brain injury on the right side (p=0.046). The volume of hemorrhage in the delirious group was larger by about 95 mL compared to the non-delirious group, but this difference was not statistically significant (p=0.382).
Conclusion: Patients with delirium after TBI had significantly different injury site and side, but not lesion size compared to patients without delirium.
Mitral Paravalvular Leak 3D Printing from 3D-Transesophageal Echocardiography
Authors: Jedrzejek M, Kozlowski M, Peszek-Przybyla E, Jadczyk T, Pysz P, Wojakowski W, Smolka G.
Institution: Department of Cardiology and Structural Heart Diseases, Medical University of Silesia, Katowice, Poland.
Abstract: Background: Paravalvular leaks can be detected in almost 15% of patients after mitral valve prosthesis implantation. This complication can result in congestive heart failure and hemolysis. Despite advancements in non-invasive imaging, percutaneous closure of paravalvular leaks is not always successful. Therefore, efforts are made to improve treatment outcomes by using 3D-printed models of defects as pre-procedural support for interventional cardiologists.
Methods: Retrospectively, 3D-transesophageal echocardiography recordings of 8 patients with clinically significant mitral paravalvular leaks were analyzed. Qlab Software was used to export DICOM images of each paravalvular leak channel, including surrounding tissue. Image segmentation was performed in 3D Slicer, a free, open-source software package used for imaging research. Models were printed to actual size with the poly jet Stratasys Objet 30 printer with a transparent, rigid material.
Results: Duration of model preparation and printing, as well as the total cost, was calculated. Mean total time of model preparation was 430.5 ± 196 minutes.
Conclusion: 3D-printing from 3D-transesophageal echocardiography is technically feasible. Both shape and location of paravalvular leaks are preserved during model preparation and printing. It remains to be tested if 3D-printing would improve outcomes of percutaneous paravalvular leaks closure.
Prediction of Ki-67 Expression in Gastrointestinal Stromal Tumors Using Radiomics of Plain and Multiphase Contrast-Enhanced CT
Publication: Eur Radiol. 2023 Jun 2. PMID: 37266658
Authors: Liu Y, He C, Fang W, Peng L, Shi F 4, Xia Y, Zhou Q, Zhang R 5, Li C.
Institution: Medical Imaging Department, Chongqing University Central Hospital, Chongqing Emergency Medical Center, Chongqing, China.
Abstract: Objective: To study the value of radiomics models based on plain and multiphase contrast-enhanced CT to predict Ki-67 expression in gastrointestinal stromal tumors (GISTs).
Methods: A total of 215 patients with GISTs were retrospectively analyzed, including 150 patients in one hospital as the training set and 65 patients in another hospital as the external verification set. The tumor at the largest level of CT images was delineated as the region of interest (ROI). The maximum diameter of the ROI was defined as the tumor size. A total of 851 radiomics features were extracted from each ROI by 3D Slicer Radiomics. After dimensionality reduction, three machine learning classification algorithms including logistic regression (LR), random forest (RF), and support vector machine (SVM) were used for Ki-67 expression prediction. Using a multivariable logistic model, a nomogram was established to predict the expression of Ki-67 individually.
Results: Delong tests showed that the SVM models had the highest accuracy in the arterial phase (Z value 0.217-1.139) and venous phase (Z value 0.022-1.396). For the plain phase, LR and SVM models had the highest accuracy (Z value 0.874-1.824, 1.139-1.763). For the delayed phase, LR models had the highest accuracy (Z value 0.056-1.824). For the combined phase, RF models had the highest accuracy (Z value 0.232-1.978). There was no significant difference among the above models for KI-67 expression prediction (Z value 0.022-1.978). A nomogram was developed with a C-index of 0.913 (95% CI, 0.878 to 0.956).
Conclusions: Radiomics of both plain and enhanced CT images could accurately predict the expression of Ki-67 in GIST. For patients who were not suitable to use contrast agents, plain scan could be used as an alternative.
Accuracy of Imaging Software for 3d Rendering of Tooth Structures, Usable in Clinical Settings
Publication: Int J Comput Dent. 2023 Jun 5;0(0):0. PMID: 37272346
Authors: Ronsivalle V, Venezia P, Migliorati M, Grippaudo C, Barbato E, Nucci L, Isola G, Leonardi RM, Lo Giudice A.
Institution: Department of General Surgery and Surgical-Medical Specialties, School of Dentistry, University of Catania, Policlinico Universitario "Vittorio Emanuele-G. Rodolico", Catania, Italy.
Abstract: Aim: The aim of this study was to evaluate the segmentation accuracy of dentition testing four free-source semi-automatic software.
Materials and methods: A total of 20 cone-beam computed tomography (CBCT) were selected to perform semi-automatic segmentation of maxillary and mandibular dentition. The software tested were Invesalius, ITK-Snap, 3D Slicer and Seg3D. Each tooth model was also manually segmented (Mimics software) and set as the gold standard (GS) reference of the investigation. A specific 3D imaging technology was used to perform the superimposition between the teeth models obtained with semi-automatic software and the GS model, and to perform the surface-to-surface matching analysis. The accuracy of semi-automatic segmentation was evaluated calculating the volumetric mean differences (mean bias and limits of agreement) and the percentage of matching of the tooth models compared to the manual segmentation (GS). Qualitative assessments were performed using color-coded maps. All data were statistically analysed to perform software comparisons.
Result: Statistically significant differences were found in the volumetric and matching percentage data (p < 0,05). Invesalius was the most accurate software for 3D rendering of the dentition with a volumetric bias (Mimics) ranging from 4,59 mm3 to 85,79 mm3; instead, ITK-SNAP showed the higher volumetric bias, ranging from 30,22 mm3 to 319,83 mm3. The dis-matched area was mainly located at the radicular region of the teeth. Volumetric data showed excellent inter-software reliability with coefficient values ranging from 0,951 to 0,997.
Conclusion: Different semi-automatic software algorithms could generate different patterns of inaccuracy error in the segmentation of teeth.
A Retrospective Three-Dimensional Study of the Mandibular Growth During Preoperative Orthodontics in Late Adolescent Patients With Skeletal Class III Malocclusion
Authors: Yuan M, Zheng Z, Li H, Wang P, Liu Y, Bi R.
Institution: State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthognathic and TMJ Surgery, West China Hospital of Stomatology, Sichuan University, China.
Abstract: Introduction: The mandible's ongoing development presents a contraindication for combined orthodontic-orthognathic treatment. The aim of this study was to evaluate the mandibular stability before and after preoperative orthodontic treatment in late adolescent patients with skeletal Class III malocclusion and to investigate the most appropriate time to start preoperative orthodontic treatment.
Material and methods: The study population consisted of 58 adolescents, aged between 15 and 21 years, with skeletal Class III malocclusion; the adolescents underwent CT scans at the beginning (T1) and the end (T2) of preoperative orthodontic treatment. The CT data were analyzed using ITK-SNAP and 3D Slicer software, and the effects of age and gender on mandibular development were investigated.
Results: In these 58 patients, there were no significant local bone alterations in the condyle and anterior chin point between T1 and T2 and no significant changes in the mandibular branch height, mandibular body length, condylar distance, and mandibular angle distance (p>0.05). The mandibular growth at the angel of mandible was statistically significant (p<0.05), but it was not clinically significant because the mean value of the growth was small (right: 0.416±0.986 mm, left: 0.328±0.886 mm). No effect of age and gender on mandibular development was observed.
Conclusion: The mandibular morphology was stable during preoperative orthodontic treatment in patients at the late adolescent stage. This study provides evidence for the possibility of early implementation of preoperative orthodontics.
Assessment of Variabilities in Lung-Contouring Methods on CBCT Preclinical Radiomics Outputs
Publication: Cancers (Basel). 2023 May 9;15(10):2677. PMID: 37345013 | PDF
Authors: Brown KH, Illyuk J, Ghita M, Walls GM, McGarry CK, Butterworth KT.
Institution: Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK.
Abstract: Radiomics image analysis has the potential to uncover disease characteristics for the development of predictive signatures and personalised radiotherapy treatment. Inter-observer and inter-software delineation variabilities are known to have downstream effects on radiomics features, reducing the reliability of the analysis. The purpose of this study was to investigate the impact of these variabilities on radiomics outputs from preclinical cone-beam computed tomography (CBCT) scans. Inter-observer variabilities were assessed using manual and semi-automated contours of mouse lungs (n = 16). Inter-software variabilities were determined between two tools (3D Slicer and ITK-SNAP). The contours were compared using Dice similarity coefficient (DSC) scores and the 95th percentile of the Hausdorff distance (HD95p) metrics. The good reliability of the radiomics outputs was defined using intraclass correlation coefficients (ICC) and their 95% confidence intervals. The median DSC scores were high (0.82-0.94), and the HD95p metrics were within the submillimetre range for all comparisons. the shape and NGTDM features were impacted the most. Manual contours had the most reliable features (73%), followed by semi-automated (66%) and inter-software (51%) variabilities. From a total of 842 features, 314 robust features overlapped across all contouring methodologies. In addition, our results have a 70% overlap with features identified from clinical inter-observer studies.
A Training Tool for Clinicians in Segmenting Medical Images to Make 3D Models
Publication: Ann Surg Open. 2023 May 23;4(2):e275. PMID: 37342255 | PDF
Authors: Chegini S, Tahim A, Liu M, Chooi Y, Edwards E, Clarkson M, Schilling C.
Institution: Department of Head and Neck Surgery, University College London Hospital, London, UK.
Abstract: Introduction: 3D models produced from medical imaging can be used to plan treatment, design prosthesis, teach and for communication. Despite the clinical benefit, few clinicians have experience of how 3D models are produced.This is the first study evaluating a training tool to teach clinicians to produce 3D models and reporting the perceived impact on their clinical practice.
Method: Following ethical approval, 10 clinicians completed a bespoke training tool, comprising written and video material alongside online support. Each clinician and 2 technicians (included as control) were sent 3 CT scans and asked to produce 6 fibula 3D models using an open-source software, 3D Slicer. The produced models were compared to those produced by the technicians using Hausdorff distance calculation. Thematic analysis was used to study the post-intervention questionnaire.
Results: The mean Hausdorff distance between the final model produced by the clinicians and technicians was 0.65mm SD0.54mm. The first model made by clinicians took a mean time of 1hr 25mins and the final model took 16:04mins (5:00-46:00mins). 100% of learners reported finding the training tool useful and will employ it in future practice.
Discussion: The training tool described in this paper is able to successfully train clinicians to produce fibula models from CT scans. Learners were able to produce comparable models to technicians within an acceptable timeframe. This does not replace technicians. However, the learners perceived this training will allow them to use this technology in more cases, with appropriate case selection and they appreciate the limits of this technology.
3D Slicer Combined With Neuroendoscope in Treatment of a Distal Segment Aneurysm of the Anterior Choroidal Artery Complicated Intraventricular Hemorrhage: A Case Report and Literature Review
Institution: Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China.
Abstract: Introduction: Pure ventricular hemorrhage is often secondary to Moyamoya disease, rarely caused by rupture of ventricular aneurysm. The surgical treatment of the latter is very challenging. 3D Slicer reconstruction technology can accurately locate small intracranial lesions and combined with minimally invasive surgery with transcranial neuroendoscope is a new attempt to treat the above diseases.
Case presentation: We report a case of pure intraventricular hemorrhage secondary to rupture of a distal segment aneurysm of the anterior choroidal artery. Brain computed tomography (CT) before admission showed pure ventricular hemorrhage, and brain CT angiography (CTA) before operation showed a distal segment aneurysm of the anterior choroidal artery. We used 3D Slicer reconstruction and precise location of the focus before the operation and used the minimally invasive surgery technique with transcranial neuroendoscope to completely remove the hematoma in the ventricle, and found the responsible aneurysm located in the ventricle.
Conclusion: Pure intraventricular hemorrhage requires vigilance against the distal segment aneurysm of the anterior choroidal artery. At present, conventional microscopic craniotomy and intravascular interventional therapy have limitations, and 3D Slicer reconstruction and precise positioning technology combined with transcranial neuroendoscope minimally invasive surgery may be a good choice.
Application of Preoperative Multimodal Image Fusion Technique in Microvascular Decompression Surgery via Suboccipital Retrosigmoid Approach
Publication: World Neurosurg. 2023 May;173:e37-e47. PMID: 36716853 | PDF
Authors: Liao CC, Wu KH, Chen G.
Institution: Department of Neurosurgery, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University,China), Zhuhai, China.
Abstract: Objective: To explore the application value of preoperative multimodal image fusion technique in microvascular decompression (MVD) surgery via the suboccipital retrosigmoid approach.
Methods: Comprehensive data of 13 patients with primary trigeminal neuralgia (TN) and 13 patients with hemifacial spasm (HFS) treated by MVD surgery via the suboccipital retrosigmoid approach at the Department of Neurosurgery in Zhuhai People's Hospital from January 2021 to December 2021 were retrospectively analyzed. Preoperatively, all patients underwent cranial thin-section computed tomography and magnetic resonance examinations. Three-dimensional (3D) digital images of the skull, brainstem, nerves, and blood vessels were constructed by the 3D Slicer software or RadiAnt DICOM Viewer, which were then applied to design the surgical approach and surgical plan. The multimodal image fusion results, clinical characteristics, intraoperative data, surgical outcomes, and complications of all patients were summarized.
Results: The 3D digital images after fusion reconstruction can vividly show the anatomical relationship between the skull, brainstem, nerves, and blood vessels and was helpful to tailor the surgical strategy. All 26 patients underwent a smooth surgery. During the surgery, the key points were accurately located, the corners of the transverse sinus and sigmoid sinus were completely exposed, and no venous sinus injury occurred in all 26 patients. The key point was approximately located at the top point of the digastric groove, 12.3 ± 0.46 mm vertically above and 6.3 ± 0.6 mm laterally to the Frankfurt horizontal plane. The average cranial opening time was 30.4 (±3.6) min, and the mean operating time was 104.7 (±12.1) min. The diameter of the bone window was about 2.0 cm-3.0 cm, and the bone flap was restored. Among the 13 patients with primary TN, 12 (92.3%) exhibited complete relief of pain and 1 had significant relief. Complications of surgery included facial sensory numbness in 1 case, vertigo in 2 cases, and herpes at the corners of the mouth in 1 case. Of the 13 patients with HFS, 12 (92.3%) had complete relief of facial twitching symptoms and 1 had significant relief, and the complications included mild facial palsy in 2 (15.4%) cases and facial sensory numbness in another 2 (15.4%) cases. The mean follow-up time after surgery ranged from 6-16 months, and 1 of 26 patients experienced recurrence of HFS during the follow-up period.
Conclusions: Preoperative multimodal image fusion technology can provide adequate preoperative assessment for patients and assistance in designing surgical approaches, which is an important guideline for MVD surgery via the suboccipital retrosigmoid approach for primary TN and facial muscle spasm.
An Interactive App with Multi-parametric MRI - Whole-Mount Histology Correlation for Enhanced Prostate MRI Training of Radiology Residents
Authors: Chatterjee A, Szasz T, Munakami M, Karademir I, Yusufishaq MS, Martens S, Wheeler C, Antic T, Thomas S, Karczmar GS, Oto A.
Institution: Department of Radiology, University of Chicago, Chicago, IL, USA.
Abstract: Rationale and objectives: To validate the educational value of a newly created learning application in enhancing prostate MRI training of radiologists for detecting prostate cancer using an observer study.
Materials and methods: An interactive learning app, LearnRadiology, was developed using a web-based framework to display multi-parametric prostate MRI images with whole-mount histology for 20 cases curated for unique pathology and teaching points. Twenty new prostate MRI cases, different from the ones used in the web app, were uploaded on 3D Slicer. Three radiologists (R1: radiologist; R2, R3: residents) blinded to pathology results were asked to mark areas suspected of cancer and provide a confidence score (1-5, with 5 being high confidence level). Then after a minimum memory washout period of 1 month, the same radiologists used the learning app and then repeated the same observer study. The diagnostic performance for detecting cancers before and after accessing the learning app was measured by correlating MRI with whole-mount pathology by an independent reviewer.
Results: The 20 subjects included in the observer study had 39 cancer lesions (13 Gleason 3 + 3, 17 Gleason 3 + 4, 7 Gleason 4 + 3, and 2 Gleason 4 + 5 lesions). The sensitivity (R1: 54% → 64%, P = 0.08; R2: 44% → 59%, P = 0.03; R3: 62% → 72%, P = 0.04) and positive predictive value (R1: 68% → 76%, P = 0.23; R2: 52% → 79%, P = 0.01; R3: 48% → 65%, P = 0.04) for all 3 radiologists improved after using the teaching app. The confidence score for true positive cancer lesion also improved significantly (R1: 4.0 ± 1.0 → 4.3 ± 0.8; R2: 3.1 ± 0.8 → 4.0 ± 1.1; R3: 2.8 ± 1.2 → 4.1 ± 1.1; P < 0.05).
Conclusion: The web-based and interactive LearnRadiology app learning resource can support medical student and postgraduate education by improving diagnostic performance of trainees for detecting prostate cancer.
3D Printed Guide Tube System for Acute Neuropixels Probe Recordings in Non-Human Primates
Publication: J Neural Eng. 2023 May 11;20(3):036009. PMID: 37105161 | PDF
Authors: Bauer DL, Pobiel B, Hilber K, Verma AK, Wang J, Vitek J, Johnson M, Johnson L.
Institution: Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA.
Abstract: Objective. Neuropixels (NP) probes are a significant advance in electrophysiological recording technology that enable monitoring of hundreds of neurons in the brain simultaneously at different depths. Application of this technology has been predominately in rodents, however widespread use in non-human primates (NHPs) such as rhesus macaques has been limited. In this study we sought to overcome two overarching challenges that impede acute NP implantation in NHPs: (1) traditional microdrive systems that mount to cephalic chambers are commonly used to access cortical areas for microelectrode recordings but are not designed to accommodate NP probes, and (2) NHPs have thick dura mater and tissue growth within the cephalic chambers which poses a challenge for insertion of the extremely fragile NP probe. Approach. In this study we present a novel NP guide tube system that can be adapted to commercial microdrive systems and demonstrate an implant method using the NP guide tube system. This system was developed using a combination of CAD design, 3D printing, and small part machining. Software programs, 3D Slicer and SolidWorks were used to target cortical areas, approximate recording depths and locations, and for in-silico implant testing. Main results. We performedin vivotesting to validate our methodology, successfully implanting, explanting, and reimplanting NP probes. We collected stable neurophysiological recordings in the premotor cortex of a rhesus macaque at rest and during performance of a reaching task.Significance.In this study we demonstrate a robust Neuropixels implant system that allows multiple penetrations with the same NP probe and share design files that will facilitate the adoption of this powerful recording technology for NHP studies.
Diagnostic Value of 18F-FDG PET/CT-Based Radiomics Nomogram in Bone Marrow Involvement of Pediatric Neuroblastoma
Publication: Acad Radiol. 2023 May;30(5):940-51. PMID: 36117128
Authors: Feng L, Yang X, Lu X, Kan Y, Wang C, Zhang H, Wang W, Yang J.
Institution: Department of Nuclear Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
Abstract: Objectives: To develop and validate an 18F-FDG PET/CT-based radiomics nomogram and evaluate the value of the 18F-FDG PET/CT-based radiomics nomogram for the diagnosis of bone marrow involvement (BMI) in pediatric neuroblastoma.
Materials and methods: A total of 144 patients with neuroblastoma (100 in the training cohort and 44 in the validation cohort) were retrospectively included. The PET/CT images of patients were visually assessed. The results of bone marrow aspirates or biopsies were used as the gold standard for BMI. Radiomics features and conventional PET parameters were extracted using 3D Slicer. Features were selected by the least absolute shrinkage and selection operator regression, and radiomics signature was constructed. Univariate and multivariate logistic regression analyses were applied to identify the independent clinical risk factors and construct the clinical model. Other different models, including the conventional PET model, combined PET-clinical model and combined radiomics model, were built using logistic regression. The combined radiomics model was based on clinical factors, conventional PET parameters and radiomics signature, which was presented as a radiomics nomogram. The diagnostic performance of the different models was evaluated by receiver operating characteristic (ROC) curves and decision curve analysis (DCA).
Results: By visual assessment, BMI was observed in 80 patients. Four conventional PET parameters (SUVmax, SUVmean, metabolic tumor volume, and total lesion glycolysis) were extracted. And 15 radiomics features were selected to build the radiomics signature. The 11q aberration, neuron-specific enolase and vanillylmandelic acid were identified as the independent clinical risk factors to establish the clinical model. The radiomics nomogram incorporating the radiomics signature, the independent clinical risk factors and SUVmean demonstrated the best diagnostic value for identifying BMI, with an area under the curve (AUC) of 0.963 and 0.931 in the training and validation cohorts, respectively. And the DCA demonstrated that the radiomics nomogram was clinically useful.
Conclusion: The 18F-FDG PET/CT-based radiomics nomogram which incorporates radiomics signature, independent clinical risk factors and conventional PET parameters could improve the diagnostic performance for BMI of pediatric neuroblastoma without additional medical costs and radiation exposure.
Opportunistic Screening for Osteoporosis Using CT Scans of the Knee: A Pilot Study
Authors: Elmahdy M, Sebro R.
Institution: Department of Radiology, Mayo Clinic, Jacksonville, FL, USA.
Abstract: Knee CT scans are used for planning for total knee arthroplasties in patients who are often simultaneously at risk for frailty fractures due to low bone mineral density. We retrospectively identified 200 patients (85.5% female) with concurrent CT scans of the knee and Dual energy x-ray absorptiometry (DXA). The mean CT attenuation of the distal femur, proximal tibia and fibula, and patella, were calculated using volumetric 3-dimensional segmentation using 3D Slicer. Data were split randomly into training 80% and test 20% datasets. The optimal CT attenuation threshold for the proximal fibula was obtained in the training dataset and evaluated in the test dataset. A support vector machine (SVM) with radial basis function (RBF) using C-classification was trained and tuned using 5-fold cross-validation in the training dataset and then evaluated in the test dataset. The SVM had a higher area-under-the curve (AUC) of 0.937 and better performance to detect osteoporosis/osteopenia than the CT attenuation of the fibula (AUC of 0.717) (P=0.015). Opportunistic screening for osteoporosis/osteopenia could be accomplished using CT scans of the knee.
Sustainable 3D Printing of Oral Films With Tunable Characteristics Using CMC-Based Inks From Durian Rind Wastes
Authors: Panraksa P, Rachtanapun P, Thipchai P, Lesniewska E, Brachais CH, Debeaufort F, Chambin O, Jantrawut P.
Institution: Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand.
Abstract: With the growing interest in environmentally friendly and personalized medicines, new concept for combining three-dimensional printing (3DP) with natural-based biomaterials derived from agro-food wastes has emerged. This approach provides sustainable solutions for agricultural waste management and potential for developing of novel pharmaceutical products with tunable characteristics. This work demonstrated the feasibility of fabricating personalized theophylline films with four different structures (Full, Grid, Star, and Hilbert) using syringe extrusion 3DP and carboxymethyl cellulose (CMC) derived from durian rind wastes. Our findings suggested that all the CMC-based inks with shear thinning properties capable of being extruded smoothly through a small nozzle could potentially be used to fabricate the films with various complex printing patterns and high structural fidelity. The results also demonstrated that the film characteristics and release profiles could be easily modified by simply changing the slicing parameters (e.g., infill density and printing pattern). Amongst all formulations, Grid film, which was 3D-printed with 40 % infill and a grid pattern, demonstrated a highly porous structure with high total pore volume. The voids between printing layers in Grid film increased theophylline release (up to 90 % in 45 min) through improved wetting and water penetration. All findings in this study provide significant insight into how to modify film characteristics simply by digitally changing the printing pattern in 3D Slicer software without creating a new CAD model. This approach could help to simplify the 3DP process so that non-specialist users can easily implement it in community pharmacies or hospital on demand.
An Automated Landmark Method to Describe Geometric Changes in the Human Mandible During Growth
Publication: Arch Oral Biol. 2023 May;149:105663. PMID: 36893681
Authors: Fournier G, Maret D, Telmon N, Savall F.
Institution: Faculté de Chirurgie Dentaire, Université Paul Sabatier, Centre Hospitalier Universitaire, Toulouse, France.
Abstract: Objective: The principal aim of this study was to assess an automatic landmarking approach to human mandibles based on the atlas method. The secondary aim was to identify the areas of greatest variation in the mandibles of middle-aged to older adults.
Design: Our sample consisted of 160 mandibles from computed tomography scans of 80 men and 80 women aged between 40 and 79 years. Eleven anatomical landmarks were placed manually on mandibles. The automated landmarking through point cloud alignment and correspondence (ALPACA) method implemented in 3D Slicer was used to automatically place landmarks to all meshes. Euclidean distances, normalized centroid size, and Procrustes ANOVA were calculated for both methods. A pseudo-landmarks approach was followed using ALPACA to identify areas of changes among our sample.
Results: The ALPACA method showed significant differences in Euclidean distances for all landmarks compared to the manual method. A mean Euclidean distance of 1.7 mm was found for the ALPACA method and 0.99 mm for the manual method. Both methods found that sex, age, and size had a significant effect on mandibular shape. The greatest variations were observed in the condyle, ramus, and symphysis regions.
Conclusion: The results obtained using the ALPACA method are acceptable and promising. This approach can automatically place landmarks with an average accuracy of less than 2 mm, which may be sufficient in most anthropometric analyses. In the light of our results, however, odontological application such as occlusal analysis is not recommended.
Three-Dimensional Volume Rendering of Pelvic Floor Anatomy with Focus on Fibroids in Relation to the Lower Urogenital Tract Based on Cross-Sectional MRI Images
Authors: Fan KS, Durnea C, Nygaard CC, Khalil M, Doumouchtsis SK.
Institution: Institute for Medical and Biomedical Education, St. George's University of London, London, UK.
Abstract: We aimed to assess the feasibility of developing three-dimensional (3D) models of pelvic organs using cross-sectional MRI images of patients with uterine fibroids and urinary symptoms and of obtaining anatomical information unavailable in 2D imaging modalities. We also aimed to compare two image processing applications. We performed a feasibility study analysing MRI scans from three women, aged 30 to 58 years old, with fibroids and urinary symptoms. Cross-sectional images were used to render 3D models of pelvic anatomy, including bladder, uterus and fibroids, using 3D Slicer and OsiriX. Dimensions, volumes and anatomical relationships of the pelvic organs were evaluated. Comparisons between anatomical landmarks and measurements obtained from the two image processing applications were undertaken. Rendered 3D pelvic models yielded detailed anatomical information and data on spatial relationships that were unobtainable from cross-sectional images. Models were rendered in sufficient resolution to aid understanding of spatial relationships between urinary bladder, uterus and fibroid(s). Measurements of fibroid volumes ranged from 5,336 to 418,012 mm3 and distances between the fibroid and urinary bladder ranged from 0.10 to 83.60 mm. Statistical analysis of measurements showed no significant differences in measurements between the two image processing applications. To date, limited data exist on the use of 3D volume reconstructions of routine MRI scans, to investigate pelvic pathologies such as fibroids in women with urinary symptoms. This study suggests that post-MRI image processing can provide additional information over standard MRI. Further studies are required to assess the role of these data in clinical practice, surgical planning and training. Three-dimensional reconstruction of routine two-dimensional magnetic resonance imaging provides additional anatomical information and may improve our understanding of anatomical relationships, their role in clinical presentations and possibly guide clinical and surgical management.
The First Endovascular Rat Glioma Model for Pre-Clinical Evaluation of Intra-Arterial Therapeutics
Authors: Lim J, Baig AA, Donnelly BM, Chaves LD, Pol SU, Koenigsknecht C, Pionessa D, Levy BR, Gutierrez L, Tutino VM, Levy EI, Siddiqui AH.
Institution: Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
Abstract: Background: Several translational animal models have been described assessing intra-arterial (IA) treatments for malignant gliomas. We describe the first endovascular animal model that allows testing of IA drug delivery as a first-line treatment, which is difficult to do in actual patients. We report a unique protocol for vascular access and IA delivery in the rat model that, unlike prior reports, does not require direct puncture and opening of proximal cerebrovasculature which carries risk of ischemia in the animal brain post-delivery.
Methods: Wistar rats underwent left femoral artery catherization with a Balt Magic 1.2F catheter or Marathon Flow directed 1.5F Microcatheter with an Asahi Chikai 0.008 micro-guidewire which was navigated to the left internal carotid artery under x-ray. 25% mannitol was administered to test blood brain barrier breakdown (BBBB). Additional rats were implanted with C6 glioma cells in the left frontal lobe. C6 Glioma-Implanted Rats (C6GRs) were monitored for overall survival and tumor growth. Tumor volumes from MRI images were calculated utilizing 3D Slicer. Additional rats underwent femoral artery catheterization with Bevacizumab, carboplatin, or irinotecan injected into the left internal carotid artery to test feasibility and safety.
Results: A successful endovascular access and BBBB protocol was established. BBBB was confirmed with positive Evans blue staining. 10 rats were successfully implanted with C6 gliomas with confirmed growths on MRI. Overall survival was 19.75 ± 2.21 days. 5 rats were utilized for the development of our femoral catheterization protocol and BBBB testing. With regards to IA chemotherapy dosage testing, control rats tolerated targeted 10 mg/kg of bevascizumab, 2.4 mg/kg of carboplatin, and 15 mg/kg of irinotecan IA ICA injections without any complications.
Conclusions: We present the first endovascular IA rat glioma model that allows selective catheterization of the intracranial vasculature and assessment of IA therapies for gliomas without need for access and sacrifice of proximal cerebrovasculature.
Muscle Magnetic Resonance Characterization of STIM1 Tubular Aggregate Myopathy Using Unsupervised Learning
Publication: PLoS One. 2023 May 8;18(5):e0285422. PMID: 37155641 | PDF
Authors: Lupi A, Spolaor S, Favero A, Bello L, Stramare R, Pegoraro E, Nobile MS.
Institution: Institute of Radiology, Department of Medicine-DIMED, University of Padua, Padua, Italy.
Abstract: Purpose: Congenital myopathies are a heterogeneous group of diseases affecting the skeletal muscles and characterized by high clinical, genetic, and histological variability. Magnetic Resonance (MR) is a valuable tool for the assessment of involved muscles (i.e., fatty replacement and oedema) and disease progression. Machine Learning is becoming increasingly applied for diagnostic purposes, but to our knowledge, Self-Organizing Maps (SOMs) have never been used for the identification of the patterns in these diseases. The aim of this study is to evaluate if SOMs may discriminate between muscles with fatty replacement (S), oedema (E) or neither (N).
Methods: MR studies of a family affected by tubular aggregates myopathy (TAM) with the histologically proven autosomal dominant mutation of the STIM1 gene, were examined: for each patient, in two MR assessments (i.e., t0 and t1, the latter after 5 years), fifty-three muscles were evaluated for muscular fatty replacement on the T1w images, and for oedema on the STIR images, for reference. Sixty radiomic features were collected from each muscle at t0 and t1 MR assessment using 3D Slicer software, in order to obtain data from images. A SOM was created to analyze all datasets using three clusters (i.e., 0, 1 and 2) and results were compared with radiological evaluation.
Results: Six patients with TAM STIM1-mutation were included. At t0 MR assessments, all patients showed widespread fatty replacement that intensifies at t1, while oedema mainly affected the muscles of the legs and appears stable at follow-up. All muscles with oedema showed fatty replacement, too. At t0 SOM grid clustering shows almost all N muscles in Cluster 0 and most of the E muscles in Cluster 1; at t1 almost all E muscles appear in Cluster 1.
Conclusion: Our unsupervised learning model appears to be able to recognize muscles altered by the presence of edema and fatty replacement.
Quantifying the Effect of an Endo-Vaginal Probe on Position of the Pelvic Floor Viscera and Muscles
Publication: Int Urogynecol J. 2023 May 5. PMID: 37145123
Authors: Chill HH, Martin LC, Abramowitch SD, Rostaminia G.
Institution: Female Pelvic Medicine and Reconstructive Surgery (FPMRS) Division, University of Chicago Pritzker School of Medicine, Northshore University HealthSystem, Skokie, IL, USA.
Abstract: Introduction and hypothesis: Endovaginal ultrasound has long been hypothesized to have a significant effect on locations of what it visualizes. However, little work has directly quantified its effect. This study aimed to quantify it.
Methods: This cross-sectional study consisted of 20 healthy asymptomatic volunteers who underwent both endovaginal ultrasound and MRI. The urethra, vagina, rectum, pelvic floor, and pubic bone were segmented in both ultrasound and MRI using 3D Slicer. Then, using 3D Slicer's transform tool the volumes were rigidly aligned based on the posterior curvature of the pubic bone. The organs were then split into thirds along their long axis to compare their distal, middle, and proximal sections. Using Houdini, we compared the location of the centroid of each of the urethra, vagina, and rectum and the surface-to-surface difference of the urethra and rectum. The anterior curvature of the pelvic floor was also compared. Normality of all variables was assessed by Shapiro-Wilk test.
Results: The largest amount of surface-to-surface distance was observed in the proximal region for the urethra and rectum. Across all three organs, the majority of the deviation was in the anterior direction for geometries obtained from ultrasound versus those from MRI. For each subject, the trace defining the midline of the levator plate was more anterior for ultrasound compared to MRI.
Conclusions: While it has often been assumed that placing a probe in the vagina probably distorts the anatomy, this study quantified the distortion and displacement of the pelvic viscera. This allows for better interpretation of clinical and research findings based on this modality.
Laser Interstitial Thermal Therapy in the Treatment of Brain Metastases: The Relationship Between Changes in Postoperative Magnetic Resonance Imaging Characteristics and Tumor Recurrence
Authors: Xue Z, Guan X, Yuan L, Kang P, Zhang C, Li D, Jia G, Jia W.
Institution: Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, China.
Abstract: Background: Laser interstitial thermal therapy (LITT) has been used to treat brain metastases (BMs) in several countries, and its safety and effectiveness have been confirmed. In most cases, magnetic resonance imaging (MRI) reveals an increase in tumor volume with an enhanced margin after LITT. However, little is known about the relationship between this MRI change and tumor recurrence.
Objective: We report the first case series of BMs treated by LITT in China to evaluate the clinical characteristics and predictive factors of tumor recurrence.
Material and Methods: Patients with less than four brain metastatic lesions and a Karnofsky performance status (KPS) > 70 were eligible for study inclusion. Standard LITT procedures were performed, and a follow-up MRI was performed to analyze the radiographic changes, especially the volume ratio of the enhanced margin and the whole lesion on MRI at 30 days postoperatively. All the volume-related data were delineated and calculated using 3D Slicer software. Related predictors were also collected to evaluate the correlation with local tumor control.
Results: Eighteen patients with nineteen lesions were enrolled for treatment and follow-up. Primary tumor histology included pulmonary carcinoma (n = 11) and breast cancer (n = 4). On average, the tumor size measured 3.01 cm3 (range, 0.40-7.40 cm3), the total ablation time was 13.58 min (range, 2.88-37.15 min), and the complete ablation rate was 92.4% (range, 29.2-100%). Comparing 3s0-day follow-up MRI results with preoperative MRI findings, 18 lesions showed a 2.28-fold (range, 1.21-4.88) volume increase; all the lesions displayed an enhanced component with a volume ratio of 42.35% (range, 10.14-100%). Five patients experienced tumor recurrence, and the local tumor control rates at 90 days and 180 days of follow-up were 68.4% and 66.7%, respectively. Univariate analysis indicated that the primary tumor, ablation rate, and enhanced volume ratio (EVR) > 40% in the 30-day MRI were associated with tumor recurrence, whereas multivariate analysis showed that only EVR > 40% was a predictive factor of local control.
Conclusion: LITT is a minimally invasive method used to ablate brain metastases which can be used as the first-line treatment for BM patients under certain indications. After LITT, most tumors showed volume enlargement on the 30-day MRI scan, and EVR > 40% on the 30-day MRI may indicate late tumor recurrence.
Image Data and Computational Grids for Computing Brain Shift and Solving the Electrocorticography Forward Problem
Institution: Intelligent Systems for Medicine Laboratory, The University of Western Australia, 35 Stirling Highway, Perth, WA, Australia.
Abstract: This article describes the dataset applied in the research reported in NeuroImage article "Patient-specific solution of the electrocorticography forward problem in deforming brain"  that is available for download from the Zenodo data repository (https://zenodo.org/record/7687631) . Preoperative structural and diffusion-weighted magnetic resonance (MR) and postoperative computed tomography (CT) images of a 12-year-old female epilepsy patient under evaluation for surgical intervention were obtained retrospectively from Boston Children's Hospital. We used these images to conduct the analysis at The University of Western Australia's Intelligent Systems for Medicine Laboratory using SlicerCBM , our open-source software extension for the 3D Slicer medical imaging platform. As part of the analysis, we processed the images to extract the patient-specific brain geometry; created computational grids, including a tetrahedral grid for the meshless solution of the biomechanical model and a regular hexahedral grid for the finite element solution of the electrocorticography forward problem; predicted the postoperative MRI and DTI that correspond to the brain configuration deformed by the placement of subdural electrodes using biomechanics-based image warping; and solved the patient-specific electrocorticography forward problem to compute the electric potential distribution within the patient's head using the original preoperative and predicted postoperative image data. The well-established and open-source file formats used in this dataset, including Nearly Raw Raster Data (NRRD) files for images, STL files for surface geometry, and Visualization Toolkit (VTK) files for computational grids, allow other research groups to easily reuse the data presented herein to solve the electrocorticography forward problem accounting for the brain shift caused by implantation of subdural grid electrodes.
ImFinite Element Analysis of a Healthy Knee Joint at Deep Squatting for the Study of Tibiofemoral and Patellofemoral Contact
Publication: J Orthop. 2023 Apr 21;40:7-16. PMID: 37143926
Institution: Department of Mechanical Engineering, K. J. Somaiya College of Engineering, Mumbai, India.
Abstract: Background: In non-western countries, deep squatting is a daily activity, and prolonged deep squatting is common among occupational squatters. Household tasks, taking a bath, socializing, using toilets, and performing religious acts are among the activities frequently carried out while squatting by the Asian population. High knee loading is responsible for a knee injury and osteoarthritis. Finite element analysis is an effective tool to determine stresses on the knee joint.
Methods: Magnetic Resonance Imaging (MRI) and Computed Tomographic (CT) images were acquired of one adult without knee injuries. The CT images were acquired at the fully extended knee and one more set of images was acquired with the knee at a deeply flexed knee position. The MRI was acquired with the fully extended knee. 3 Dimensional models of bones were created using CT and soft tissue using MRI with the help of 3D Slicer software. Kinematics and finite element analysis of the knee was performed for standing and deep squatting posture using Ansys Workbench 2022.
Results: High peak stresses were observed at deep squatting compared to standing along with the reduction in the contact area. Peak von Mises stresses on femoral cartilage, tibial cartilage, patellar cartilage, and meniscus were increased from 3.3 MPa to 19.9 MPa, 2.9 MPa to 12.4 MPa, 1.5 MPa to 16.7 MPa and 15.8 MPa to 32.8 MPa respectively during deep squatting. Posterior translation of 7.01 mm, and 12.58 mm was observed for medial and lateral femoral condyle respectively from full extension to 153° knee flexion.
Conclusions: Increased stresses in the knee joint at deep squat posture may cause cartilage damage. A sustained deep squat posture should be avoided for healthy knee joints. More posterior translations of the medial femoral condyle at higher knee flexion angle warrant further investigation.
A Comparison of Machine Learning Models for Survival Prediction of Patients with Glioma Using Radiomic Features from MRI Scans
Authors: Manjunath M, Saravanakumar S, Kiran S, Chatterjee J.
Institution: Department of Biotechnology, People's Education Society University, Bangalore, Karnataka, India.
Abstract: Background Glioma is a primary, malignant, highly aggressive brain tumor, with patients having an average life expectancy of 14 to 16 months after diagnosis. Magnetic resonance imaging (MRI) scans of these patients can be used to extract and analyze quantifiable features with potential clinical significance. We hypothesize that there is a correlation between radiomic features extracted from MRI scans and survival. Along with clinical data, the radiomic features could be used in survival prediction of patients, providing beneficial information for clinicians to design personalized treatment plans. Methods In our study, we have utilized 3D Slicer for tumor segmentation and feature extraction and performed survival prediction of patients with glioma using four different machine learning models. Results and Conclusion Among the models compared, we have achieved a maximum prediction accuracy of 64.4% using the k-nearest neighbors model, which was trained and tested on a combination of clinical data and radiomic features extracted from MRI images provided in the BraTS 2020 dataset.
Circular RNA hsa_circ_0000690 as a Potential Biomarker for Diagnosis and Prognosis of Intracranial Aneurysm: Closely Relating to the Volume of Hemorrhage
Authors:Huang Y, Cao H, Qi X, Guan C, Que S.
Institution: Department of Neurosurgery, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, Fujian, China.
Purpose: This study aimed to explore circular RNA (circRNA) hsa_circ_0000690 as a potential biomarker for diagnosis and prognosis of intracranial aneurysm (IA) and its relationship with clinical factors and complications of IA.
Material/Methods: 216 IA patients admitted to the neurosurgery department of our hospital from January 2019 to December 2020 were selected as the experimental group, and 186 healthy volunteers were selected as the control group. The expression of hsa_circ_0000690 in peripheral blood was detected by quantitative real-time PCR, and its diagnostic value was assessed by receiver operating characteristic curve. Relationship between hsa_circ_0000690 and clinical factors of IA was assessed by chi-square test. Nonparametric test was used in univariate analysis, and regression analysis was used in multivariate analysis. Multivariate Cox proportional hazards regression analysis was used to analyze the survival time.
Results: CircRNA hsa_circ_0000690 of IA patients was relatively lower than that in the control group (p < .001). The AUC of hsa_circ_0000690 was 0.752, the specificity was 0.780, and sensitivity was 0.620, with diagnostic threshold of 0.0449. In addition, hsa_circ_0000690 expression was correlated with Glasgow Coma Scale, the volume of subarachnoid hemorrhage, modified Fisher scale, Hunt-Hess levels and surgical type. For hydrocephalus and delayed cerebral ischemia, hsa_circ_0000690 was significant in univariate analysis, but nonsignificant in multivariate analysis. For prognosis, hsa_circ_0000690 was significantly associated with modified Rankin Scales after surgery for 3 months, but not associated with survival time.
Conclusions: The expression of hsa_circ_0000690 can act as a diagnostic marker for IA and predict the prognosis of 3 months after operation and is closely related to the volume of hemorrhage.
Keywords: 3D Slicer; biomarker; circRNA; diagnosis; intracranial aneurysm; prognosis; subarachnoid hemorrhage
Can Quantitative Peritumoral CT Radiomics Features Predict the Prognosis of Patients With Non-Small Cell Lung Cancer? A Systematic Review
Publication: Eur Radiol. 2023 Mar;33(3):2105-17. PMID: 36307554 | PDF
Authors: Wu L, Lou X, Kong N, Xu M, Gao C.
Institution: Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
Abstract: Objectives: To provide an overarching evaluation of the value of peritumoral CT radiomics features for predicting the prognosis of non-small cell lung cancer and to assess the quality of the available studies.
Methods: The PubMed, Embase, Web of Science, and Cochrane Library databases were searched for studies predicting the prognosis in patients with non-small cell lung cancer (NSCLC) using CT-based peritumoral radiomics features. Information about the patient, CT-scanner, and radiomics analyses were all extracted for the included studies. Study quality was assessed using the Radiomics Quality Score (RQS) and the Prediction Model Risk of Bias Assessment Tool (PROBAST).
Results: Thirteen studies were included with 2942 patients from 2017 to 2022. Only one study was prospective, and the others were all retrospectively designed. Manual segmentation and multicenter studies were performed by 69% and 46% of the included studies, respectively. 3D Slicer and MATLAB software were most commonly used for the segmentation of lesions and extraction of features. The peritumoral region was most frequently defined as dilated from the tumor boundary of 15 mm, 20 mm, or 30 mm. The median RQS of the studies was 13 (range 4-19), while all of included studies were assessed as having a high risk of bias (ROB) overall.
Conclusions: Peritumoral radiomics features based on CT images showed promise in predicting the prognosis of NSCLC, although well-designed studies and further biological validation are still needed.
Key points: Peritumoral radiomics features based on CT images are promising and encouraging for predicting the prognosis of non-small cell lung cancer. The peritumoral region was often dilated from the tumor boundary of 15 mm or 20 mm because these were considered safe margins. The median Radiomics Quality Score of the included studies was 13 (range 4-19), and all of studies were considered to have a high risk of bias overall.
Three Dimensional Assessment of Radiographic Changes after Indirect Pulp Capping using Silver Diamine Fluoride with or without Potassium Iodide in Young Permanent Teeth (12-month RCT)
Publication: Caries Res. 2023;57(2):177-188. PMID: 36878216
Authors: Baraka MMAL, Cevidanes L, Tekeya M, Bakry N, Ruellas A, Botero T, Benavides E, Fontana M.
Institution: Department of Experimental Oncology, European Institute of Oncology, IRCCS, 20139 Milan, Italy.
Abstract: The aim was to have a three-dimensional evaluation of radiographic changes after indirect pulp capping (IPC) with silver diamine fluoride (SDF) with or without potassium iodide (KI) and resin modified glass ionomer cement (RMGIC) in deep carious young permanent molars using cone beam computed tomography (CBCT). 108 first permanent molars with deep occlusal cavitated caries lesions, in forty-nine 6-9-year-old children, were randomly allocated to one of 3 groups (n=36) and treated with SDF+KI, SDF and RMGIC as IPC materials. CBCT scans were taken at 0 and at 12-months to assess tertiary dentin formation (volume and grey level intensity), increase in root length, and pathological changes as secondary caries, periapical radiolucency, internal resorption and obliteration of the pulp. The three-dimensional image analysis procedures were performed using ITK-SNAP and 3D Slicer CMF. Comparisons were made using analysis of variance with a fixed effect for treatment and random effects for patient, and patient-by-treatment to account for within-patient correlations. A two-sided 5% significance level was used. There were no significant differences among the three groups regarding tertiary dentin volume (p=0.712) and grey level intensity (p=0.660), increase in root length (p=0.365), prevention of secondary caries (p=0.63) and periapical radiolucency (p=0.80) in the analysed 69 CBCT scans. The study did not find differences among the groups regarding quality and quantity of tertiary dentin formed, increase in root length, absence of secondary caries and other signs of failure as shown by CBCT.
Clinical Significance: The results show no significant differences in radiographic outcomes (quality and quantity of tertiary dentin formed, increase in root length, absence of secondary caries and other signs of failure) when using SDF+KI, SDF and RMGIC in IPC. The results of this study can help guide treatment decision making regarding use of SDF and SDF+KI as IPC materials in deep cavitated lesions.
Cross-Sectional Reliability and Concurrent Validity of a Quantitative 2-Dimensional Ultrasound Image Analysis of Effusion and Synovial Hypertrophy in Knee Osteoarthritis
Institution: Faculty of Health Sciences, University of Western Ontario, London, ON, Canada.
Abstract: Objective: Effusion-synovitis is related to pain and progression in knee osteoarthritis (OA), but current gold standard ultrasound (US) measures are limited to semi-quantitative grading of joint distension or 1-dimensional thickness measures. A novel quantitative 2-dimensional image analysis methodology is applied to US images of effusion-synovitis; reliability and concurrent validity was assessed in patients with knee OA.
Methods: Cross sectional analysis of US images collected from 51 patients with symptomatic knee OA were processed in ImageJ and segmented in 3D Slicer to produce a binary mask of the supra-patellar synovitis region of interest (ROI). Area measures (mm2) of total synovitis, effusion and hypertrophy components were exported. Intra-rater reliability and test-retest reliability (1-14 days washout) were estimated with intra-class correlation coefficients (ICCs). Concurrent validity was measured by Spearman correlations between quantitative measures and gold standard OMERACT and caliper measurements of synovitis.
Results: Intra-rater reliability for hypertrophy area was estimated at 0.98, 0.99 for effusion area, and 0.99 for total synovitis area. The test-retest reliability for total synovitis area was 0.63 (SEM 87.8 mm2), 0.59 for hypertrophy area (SEM 21.0 mm2), and 0.64 for effusion area (SEM 73.8 mm2). Correlation between total synovitis area and OMERACT grade was 0.84, 0.81 between total synovitis area and effusion-synovitis calipers, and 0.81 between total effusion area and effusion calipers.
Conclusion: This new research tool for image analysis demonstrated excellent intra-rater reliability, good concurrent validity, and moderate test-retest reliability. Quantitative 2D US measures of effusion-synovitis and its individual components may enhance the study and management of knee OA.
Patient-Specific Needle Guidance Templates Drilled Intraprocedurally for Image Guided Intervention: Feasibility Study in Swine
Authors: Glossop N, Bale R, Xu S, Pritchard WF, Karanian JW, Wood BJ.
Institution: Queen's University, Kingston, ON, Canada.
Abstract: purpose: Thermal ablation of large tumors may benefit from simultaneous placement of multiple needles, but accurate placement becomes challenging as the number of needles increases. The aim of this work was to evaluate use of personalized needle guidance grid templates based on intraprocedural CT and fabricated at the point of care to implement ablation treatment plans with multiple needles in vivo.
Methods: A plastic frame was designed to hold two parallel plastic guide plates in a rigid relationship, fixed over the abdomen by a mounting arm. Steel ball targets (1.5 mm) were implanted under ultrasound in the livers of two domestic swine under general anesthesia. Following breath-hold CT of the subject and frame, the targets and frame were identified using customized 3D Slicer-based planning software. Multiple needle trajectories targeting the balls were planned, including complex off-plane trajectories. A machining program for drilling the hole pattern corresponding to the planned needle trajectories was generated. The pattern was drilled in the two plates with a numerical-controlled milling machine in the suite. The plates were attached to the frame and needles passed through the paired holes to the calculated depth. Placement accuracy was defined as needle tip-to-target distance on post-placement CT.
Results: The planning process and manufacturing required approximately 6 and 15 min, respectively. Needles were rapidly inserted (n = 11) to the target points without complications or traversing nontarget anatomy. The mean needle tip-to-target distance error was 3.4 ± 2.2, range 0-7 mm.
Conclusion: Rapid and accurate needle placement was feasible using a subject-specific, custom-drilled, needle guidance grid template fabricated intraprocedurally. Targeting accuracy and performance were similar to more complex and expensive tracking systems which may enable accurate intraprocedural implementation of treatment plans in the liver or other organs. This may be of value in complex ablation cases or in areas where more advanced guidance systems are not available.
Automatic Landmark Identification in Cone-Beam Computed Tomography
Publication: Orthod Craniofac Res. 2023 Feb 21. PMID: 36811276
Authors: Gillot M, Miranda F, Baquero B, Ruellas A, Gurgel M, Al Turkestani N, Anchling L, Hutin N, Biggs E, Yatabe M, Paniagua B, Fillion-Robin JC, Allemang D, Bianchi J, Cevidanes L, Prieto JC.
Institution: Department of Orthodontics and Pediatric Dentistry, School of Dental Medicine, University of Michigan, Ann Arbor, MI, USA.
Abstract: Objective: To present and validate an open-source fully automated landmark placement (ALICBCT) tool for cone-beam computed tomography scans.
Material and Methods: One hundred and forty-three large and medium field of view cone-beam computed tomography (CBCT) were used to train and test a novel approach, called ALICBCT that reformulates landmark detection as a classification problem through a virtual agent placed inside volumetric images. The landmark agents were trained to navigate in a multi-scale volumetric space to reach the estimated landmark position. The agent movements decision relies on a combination of DenseNet feature network and fully connected layers. For each CBCT, 32 ground truth landmark positions were identified by 2 clinician experts. After validation of the 32 landmarks, new models were trained to identify a total of 119 landmarks that are commonly used in clinical studies for the quantification of changes in bone morphology and tooth position.
Results: Our method achieved a high accuracy with an average of 1.54±0.87 mm error for the 32 landmark positions with rare failures, taking an average of 4.2s computation time to identify each landmark in one large 3D-CBCT scan using a conventional GPU.
Conclusion: The ALICBCT algorithm is a robust automatic identification tool that has been deployed for clinical and research use as an extension in the 3D Slicer platform allowing continuous updates for increased precision.
Development and In-Silico and Ex-Vivo Validation of a Software for a Semi-Automated Segmentation of the Round Window Niche to Design a Patient Specific Implant to Treat Inner Ear Disorders
Authors: Matin-Mann F, Gao Z, Wei C, Repp F, Artukarslan EN, John S, Alcacer Labrador D, Lenarz T, Scheper V.
Institution: Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), Department of Otorhinolaryngology, Head and Neck Surgery, Hannover Medical School, Hannover, Germany.
Abstract: The aim of this study was to develop and validate a semi-automated segmentation approach that identifies the round window niche (RWN) and round window membrane (RWM) for use in the development of patient individualized round window niche implants (RNI) to treat inner ear disorders. Twenty cone beam computed tomography (CBCT) datasets of unilateral temporal bones of patients were included in the study. Defined anatomical landmarks such as the RWM were used to develop a customized 3D Slicer plugin for semi-automated segmentation of the RWN. Two otolaryngologists (User 1 and User 2) segmented the datasets manually and semi-automatically using the developed software. Both methods were compared in-silico regarding the resulting RWM area and RWN volume. Finally, the developed software was validated ex-vivo in N = 3 body donor implantation tests with additively manufactured RNI. The independently segmented temporal bones of the different Users showed a strong consistency in the volume of the RWN and the area of the RWM. The volume of the semi-automated RWN segmentations were 48 ± 11% smaller on average than the manual segmentations and the area of the RWM of the semi-automated segmentations was 21 ± 17% smaller on average than the manual segmentation. All additively manufactured implants, based on the semi-automated segmentation method could be implanted successfully in a pressure-tight fit into the RWN. The implants based on the manual segmentations failed to fit into the RWN and this suggests that the larger manual segmentations were over-segmentations. This study presents a semi-automated approach for segmenting the RWN and RWM in temporal bone CBCT scans that is efficient, fast, accurate, and not dependent on trained users. In addition, the manual segmentation, often positioned as the gold-standard, actually failed to pass the implantation validation.
Design and Analysis of HSC-BPPV Diagnostic Maneuver Based on Virtual Simulation
Publication: Front Neurol. 2023 Feb 17;14:1132343. PMID: 36873445 | PDF
Authors: Li Y, Yang X.
Institution: Department of Research Center, Third Affiliated Hospital of Shanghai University, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou People's Hospital, Wenzhou, China.
Abstract: Background: The preferred supine roll test for the diagnosis of horizontal semicircular canal BPPV has several disadvantages, including difficulty in locating the affected ear, inconsistent nystagmus performance on repeated testing, and lack of a typical latency period, resulting in insensitive diagnosis.
Objectives: To investigate novel diagnostic techniques with more scientific design, more accessible application, and better diagnostic sensitivity and specificity.
Materials and Methods: Based on clinical microscopic CT data, we created a virtual simulation model of BPPV using Unity software. The physical simulation of the traditional supine roll test was performed to observe and analyse the movement of the otoliths, whose initial position was the typical stable position. In addition, the normal vectors of the plane and crista ampullaris of the horizontal semicircular canal were measured using 3D Slicer software. Based on this, we analyzed the critical steps for designing diagnostic maneuvers for BPPV in the horizontal semicircular canal. For a more accurate diagnosis of horizontal semicircular canal BPPV, it is critical to rotate the horizontal semicircular canal to be parallel to gravity. It is also necessary to move the otolith by swinging the head. As a result, we developed two diagnostic maneuvers: the 60° roll test and the prone roll test. We also performed simulations to observe otolith movement and predict nystagmus performance.
Conclusions: The 60° roll test and the prone roll test can complement the supine roll test. Compared to the supine roll test, they not only effectively differentiate canalolithiasis from cupulolithiasis, but also make it easier to determine the position of the otoliths, and the characteristics of the nystagmus are more pronounced. Significant diagnostic features have significant potential benefits for home and telemedicine.
The Simplified Tailor-Made Workflows for a 3D Slicer-Based Craniofacial Implant Design
Authors: Tantisatirapong S, Khunakornpattanakarn S, Suesatsakul T, Boonpratatong A, Benjamin I, Tongmeesee S, Kangkorn T, Chanwimalueang
Institution: Department of Biomedical Engineering, Faculty of Engineering, Srinakharinwirot University, Nakhon Nayok, Thailand.
Abstract: A specific design of craniofacial implant model is vital and urgent for patients with traumatic head injury. The mirror technique is commonly used for modeling these implants, but it requires the presence of a healthy skull region opposite to the defect. To address this limitation, we propose three processing workflows for modeling craniofacial implants: the mirror method, the baffle planner, and the baffle-based mirror guideline. These workflows are based on extension modules on the 3D Slicer platform and were developed to simplify the modeling process for a variety of craniofacial scenarios. To evaluate the effectiveness of these proposed workflows, we investigated craniofacial CT datasets collected from four accidental cases. The designed implant models were created using the three proposed workflows and compared to reference models created by an experienced neurosurgeon. The spatial properties of the models were evaluated using performance metrics. Our results show that the mirror method is suitable for cases where a healthy skull region can be completely reflected to the defect region. The baffle planner module offers a flexible prototype model that can be fit independently to any defect location, but it requires customized refinement of contour and thickness to fill the missing region seamlessly and relies on the user's experience and expertise. The proposed baffle-based mirror guideline method strengthens the baffle planner method by tracing the mirrored surface. Overall, our study suggests that the three proposed workflows for craniofacial implant modeling simplify the process and can be practically applied to a variety of craniofacial scenarios. These findings have the potential to improve the care of patients with traumatic head injuries and could be used by neurosurgeons and other medical professionals.
Predicting Transient Ischemic Attack Risk in Patients With Mild Carotid Stenosis Using Machine Learning and CT Radiomics
Publication: Front Neurol. 2023 Feb 8;14:1105616. PMID: 36846119 | PDF
Authors: Xia H, Yuan L, Zhao W, Zhang C, Zhao L, Hou J, Luan Y, Bi Y, Feng Y.
Institution: Department of Vascular Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China.
Abstract: Objective: This study aims to establish a radiomics-based machine learning model that predicts the risk of transient ischemic attack in patients with mild carotid stenosis (30-50% North American Symptomatic Carotid Endarterectomy Trial) using extracted computed tomography radiomics features and clinical information.
Methods: A total of 179 patients underwent carotid computed tomography angiography (CTA), and 219 carotid arteries with a plaque at the carotid bifurcation or proximal to the internal carotid artery were selected. The patients were divided into two groups; patients with symptoms of transient ischemic attack after CTA and patients without symptoms of transient ischemic attack after CTA. Then we performed random sampling methods stratified by the predictive outcome to obtain the training set (N = 165) and testing set (N = 66). 3D Slicer was employed to select the site of plaque on the computed tomography image as the volume of interest. An open-source package PyRadiomics in Python was used to extract radiomics features from the volume of interests. The random forest and logistic regression models were used to screen feature variables, and five classification algorithms were used, including random forest, eXtreme Gradient Boosting, logistic regression, support vector machine, and k-nearest neighbors. Data on radiomic feature information, clinical information, and the combination of these pieces of information were used to generate the model that predicts the risk of transient ischemic attack in patients with mild carotid artery stenosis (30-50% North American Symptomatic Carotid Endarterectomy Trial).
Results: The random forest model that was built based on the radiomics and clinical feature information had the highest accuracy (area under curve = 0.879; 95% confidence interval, 0.787-0.979). The combined model outperformed the clinical model, whereas the combined model showed no significant difference from the radiomics model.
Conclusion: The random forest model constructed with both radiomics and clinical information can accurately predict and improve discriminative power of computed tomography angiography in identifying ischemic symptoms in patients with carotid atherosclerosis. This model can aid in guiding the follow-up treatment of patients at high risk.
Deep Learning Enabled Multi-Organ Segmentation of Mouse Embryos
Publication: Biol Open. 2023 Feb 15;12(2):bio059698. PMID: 36802342 | PDF
Authors: Rolfe SM, Whikehart SM, Maga AM.
Institution: Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA.
Abstract: The International Mouse Phenotyping Consortium (IMPC) has generated a large repository of three-dimensional (3D) imaging data from mouse embryos, providing a rich resource for investigating phenotype/genotype interactions. While the data is freely available, the computing resources and human effort required to segment these images for analysis of individual structures can create a significant hurdle for research. In this paper, we present an open source, deep learning-enabled tool, Mouse Embryo Multi-Organ Segmentation (MEMOS), that estimates a segmentation of 50 anatomical structures with a support for manually reviewing, editing, and analyzing the estimated segmentation in a single application. MEMOS is implemented as an extension on the 3D Slicer platform and is designed to be accessible to researchers without coding experience. We validate the performance of MEMOS-generated segmentations through comparison to state-of-the-art atlas-based segmentation and quantification of previously reported anatomical abnormalities in a Cbx4 knockout strain. This article has an associated First Person interview with the first author of the paper.
Development and Validation of an 18FFDG-PET/CT Radiomic Model for Predicting Progression-Free Survival for Patients With Stage II - III Thoracic Esophageal Squamous Cell Carcinoma Who Are Treated With Definitive Chemoradiotherapy
Publication: Acta Oncol. 2023 Feb;62(2):159-65. PMID: 36794365
Authors: Takahashi N, Tanaka S, Umezawa R, Takanami K, Takeda K, Yamamoto T, Suzuki Y, Katsuta Y, Kadoya N, Jingu K.
Institution: Department of Radiation Oncology, Tohoku University Graduate School of Medicine, Japan.
Abstract: Background: Radiomics is a method for extracting a large amount of information from images and used to predict treatment outcomes, side effects and diagnosis. In this study, we developed and validated a radiomic model of [18F]FDG-PET/CT for predicting progression-free survival (PFS) of definitive chemoradiotherapy (dCRT) for patients with esophageal cancer.
Material and Methods: Patients with stage II - III esophageal cancer who underwent [18F]FDG-PET/CT within 45 days before dCRT between 2005 and 2017 were included. Patients were randomly assigned to a training set (85 patients) and a validation set (45 patients). Radiomic parameters inside the area of standard uptake value ≥ 3 were calculated. The open-source software 3D Slicer and Pyradiomics were used for segmentation and calculating radiomic parameters, respectively. Eight hundred sixty radiomic parameters and general information were investigated.In the training set, a radiomic model for PFS was made from the LASSO Cox regression model and Rad-score was calculated. In the validation set, the model was applied to Kaplan-Meier curves. The median value of Rad-score in the training set was used as a cutoff value in the validation set. JMP was used for statistical analysis. RStudio was used for the LASSO Cox regression model. p < 0.05 was defined as significant.
Results: The median follow-up periods were 21.9 months for all patients and 63.4 months for survivors. The 5-year PFS rate was 24.0%. In the training set, the LASSO Cox regression model selects 6 parameters and made a model. The low Rad-score group had significantly better PFS than that the high Rad-score group (p = 0.019). In the validation set, the low Rad-score group had significantly better PFS than that the high Rad-score group (p = 0.040).
Conclusions: The [18F]FDG-PET/CT radiomic model could predict PFS for patients with esophageal cancer who received dCRT.
Minimizing Magnetic Resonance Image Geometric Distortion at 7 Tesla for Frameless Presurgical Planning Using Skin-Adhered Fiducials
Publication: Med Phys. 2023 Feb;50(2):694-701. PMID: 36301228
Authors: Kirby KM, Koons EK, Welker KM, Fagan AJ.
Institution: Department of Radiology, Mayo Clinic, Rochester, MN, USA.
Abstract: Background: 7T MRI offers significant benefits to spatial and contrast resolution compared to lower field strengths. This superior image quality can help better delineate targets in stereotactic neurosurgical procedures; however, the potential for increased geometric distortions at 7T has impaired its widespread use for these applications. Image geometric distortions can be due to distortions of B0 arising from tissue magnetic susceptibility effects or inherent field inhomogeneities, and nonlinearity of the magnetic field gradients.
Purpose: The purpose of this study was to investigate the use of 7T MRI for neurosurgical frameless stereotactic navigation procedures. Image geometric distortions at the skin surface in 7T images were minimized and compared to results from clinical 3T frameless imaging protocols.
Methods: A 3D-printed grid phantom filled with oil was designed to perform a fine calibration of the 7T imaging gradients, and an oil-filled head phantom with internal targets was used to determine ground truth (from computed tomography [CT]) positioning errors. Three volunteers and the head phantom were imaged consecutively at 3T and 7T. Ten skin-adhesive fiducial markers were placed on each subject's exposed skin surface at standard clinical placement locations for frameless procedures. Imaging sequences included MPRAGE (three bandwidths at 7T: 400, 690, and 1020 Hz/pixel, and one at 3T: 400 Hz/pixel), T2 SPACE, and T2 SPACE FLAIR acquisitions. An additional GRE field map was acquired on both scanners using a multi-echo GRE sequence. Custom Matlab code was used to perform additional distortion correction of the images using the unwrapped field maps. Fiducial localization was performed with 3D Slicer, with absolute fiducial positioning errors determined in phantom experiments following rigid registration to the CT images. For human experiments, 3T and 7T images were registered and relative differences in fiducial locations were compared using two-tailed paired t-tests.
Results: Phantom measurements at 7T yielded gradient distance scaling errors of 1.1%, 2.2%, and 1.0% along the x-, y-, and z-axes, respectively. These system miscalibrations were traced back to phantom manufacturing deviations in the sphericity of the vendor's gradient calibration phantom. Correction factors along each gradient axis were applied, and afterward, geometric distortions of less than 1 mm were obtained in the 7T MR head phantom images for the 1020 Hz/pixel bandwidth MPRAGE sequence. For the human subjects, four fiducial locations were excluded from the analysis due to patient positioning differences. Differences between 3T and 7T MPRAGE with low/medium/high bandwidth were 2.2 /2.6/2.3 mm, respectively, before the correction, reducing to 1.6/1.3/1.0 mm after the correction (p < 0.001). T2 SPACE and T2 SPACE FLAIR yielded a similar pattern when the correction was applied, decreasing from 2.1 to 0.8 mm, and 2.6 to 1.0 mm, respectively.
Conclusions: 7T MRI can be used to perform frameless presurgical planning with skin-adhesive fiducials. Geometric distortions can be reduced to a clinically relevant level (errors < ∼1 mm) with no significant susceptibility-related distortions, by using high receiver bandwidth, ensuring gradients are properly calibrated, and placing skin fiducials in areas where distortions from patient positioning are minimal.
Acute Colonic Pseudo-Obstruction Secondary to Renal Calculus: A Case Report and Review of Pathophysiology
Authors: Gillies M, AlDujaili T.
Institution: General Surgery, Goulburn Valley Health, Shepparton, Australia
Abstract: Acute colonic pseudo-obstruction (ACPO) is obstruction of the large bowel without a mechanical cause. The exact mechanism remains incompletely understood but is thought to result from disruption to the autonomic regulation of the colon, typically in the context of hospitalized patients with medical illness, precipitating medications, or recent surgical intervention. This paper presents an unusual case of ACPO in an ambulatory patient with a recently passed renal calculus, explores the anatomy and physiology underlying the autonomic dysfunction theory of ACPO pathogenesis in the context of the case, and provides a 3D reconstruction of the patient's CT to illustrate the abrupt caliber change at the splenic flexure characteristic of ACPO.
Keywords: 3d reconstruction; acute colonic pseudo-obstruction; ogilvie's syndrome; renal calculi; 3D Slicer software.
A Novel Stereotactic Aspiration Technique for Intracerebral Hemorrhage
Authors: Xu HZ, Guo J, Wang C, Liu X, Song ZQ, Chen RF, Qiu B, Wang Q, Huang Y.
Institution: Department of Neurosurgery, Civil Aviation General Hospital, Beijing, China.
Background: Minimally invasive surgery is effective and recommended for treatment of intracerebral hemorrhage; however, neurosurgeons in grass-root hospitals in underdeveloped countries lack effective and precise minimally invasive surgery techniques. The aim of this study was to present a technique of computed tomography angiography-based three-dimensional-printed navigation mold-guided stereotactic aspiration and demonstrate its clinical application using a hard needle in a series of patients.
Methods: The novel stereotactic aspiration technique was performed in 18 patients with spontaneous intracerebral hemorrhage at our center, and clinical outcomes were reported. We compared the volume of hematoma measured by 3 different methods: ABC/2 formula, manual segmentation with OsiriX, and manual segmentation with 3D Slicer.
Results: The surgery was completed safely within an average operative time of 15.11 minutes, achieving the goal of <15 mL residual clot volume or >70% clot removal in all patients. No intracranial rebleeding or infection was observed postoperatively. At the end of the 6-month follow-up, 61.11% (11/18) of patients achieved a modified Rankin Scale score <3. There was overall better agreement of hematoma measurement using segmentation with 3D Slicer rather than ABC/2 measurement or hematoma measurement using segmentation with OsiriX.
Conclusions: Our novel method of stereotactic aspiration benefited patients in this study with good percent clot removal, few surgery-related complications, and a favorable prognosis. Manual segmentation with 3D Slicer could be used to provide the neurosurgeon with dependable information about hematoma volume. This cheap and convenient technique may be applied in grass-root hospitals in underdeveloped countries. Assessment in multicenter prospective clinical trials is needed.
Morphological Evaluation of the Normal and Hydrocephalic Third Ventricle on Cranial Magnetic Resonance Imaging in Children: A Retrospective Study
Authors: Isıklar S, Turan Ozdemir S, Ozkaya G, Ozpar R, Parlak M.
Institution: Medical Imaging Techniques Program, Vocational School of Health Services, Bursa Uludag University, 16240, Bursa, Turkey.
Abstract: Background: Third ventricle morphological changes reflect changes in the ventricular system in pediatric hydrocephalus, so visual inspection of the third ventricle shape is standard practice. However, normal pediatric reference data are not available.
Objective: To investigate both the normal development of the third ventricle in the 0-18-year age group and changes in its biometry due to hydrocephalus.
Materials and Methods: For this retrospective study, we selected individuals ages 0-18 years who had magnetic resonance imaging (MRI) from 2012 to 2020. We included 700 children (331 girls) who had three-dimensional (3-D) T1-weighted sequences without and 25 with hydrocephalus (11 girls). We measured the distances between the anatomical structures limiting the third ventricle by dividing the third ventricle into anterior and posterior regions. We made seven linear measurements and three index calculations using 3DSlicer and MRICloud pipeline, and we analyzed the results of 23 age groups in normal and hydrocephalic patients using SPSS (v. 23).
Results: Salient findings are: (1) The posterior part of the third ventricle is more affected by both developmental and hydrocephalus-related changes. (2) For third ventricle measurements, gender was insignificant while age was significant. (3) Normal third ventricular volumetric development showed a segmental increase in the 0-18 age range. The hydrocephalic third ventricle volume cut-off value in this age group was 3 cm3.
Conclusion: This study describes third ventricle morphometry using a linear measurement method. The ratios defined in the midsagittal plane were clinically useful for diagnosing the hydrocephalic third ventricle. The linear and volumetric reference data and ratios are expected to help increase diagnostic accuracy in distinguishing normal and hydrocephalic third ventricles.
Henri IV of France's Larynx 3D Reconstitution
Authors: Baudouin R, Amelot A, Laprie Y, Crevier-Buchman L, Maeda S, Huynh-Charlier I, Hans S, Charlier P.
Institution: Department of Otolaryngology-Head & Neck Surgery, Foch Hospital, School of Medicine, UFR Simone Veil, Université Versailles Saint-Quentin-en-Yvelines (Université Paris Saclay), Montigny-le-Bretonneux, France.
Abstract: Objectives: King Henri IV of France (reign from 1589 to 1610) was one of the most important kings of France. Embalmed and buried in Saint-Denis, his remains were beheaded in 1793. His head (including his larynx) survived in successive private collections until its definitive identification in 2010. The purpose of the study was to provide a morphologic study of the larynx with a 3D reconstitution.
Methods: A flexible endoscopy was performed via the mouth and via the trachea. Measures of the larynx (vocal folds lengths, thickness, width, larynx height) were collected from the CT-scan by a panel of experts blind each other. The segmentation of the laryngeal anatomical components (vocal folds, cartilages) was performed using 3D Slicer. Mesh smoothing and 3D reconstitution were performed using Fusion 360®. Reconstitution was discussed between the experts. Decision was made by consensus after discussion.
Results: Cricoid, thyroid, arytenoid cartilages, vocal folds and hyoid bone were identified and a computed 3D reconstitution of the larynx was made. The laryngeal 3D model appeared morphologically similar to a living subject. Measures were similar but smaller than those of a modern subject.
Conclusions: The 3D reconstitution of the larynx of Henri IV of France was conducted from the CT-scan of his mummified head. This work constitutes a first valuable morphologic analysis of a larynx from an embalmed individual. This anatomical work is the first step towards the reconstruction of the voice of this historical character, which we hope to concretize with computer modeling tools in a second step.
Development and External Validation of a Novel Nomogram to Predict Prostate Cancer in Biopsy-Naïve Patients With PSA <10 Ng/Ml and PI-RADS v2.1 = 3 Lesions
Publication: Cancer Med. 2023 Feb;12(3):2560-71. PMID: 35920264 | PDF
Authors: Hu C, Sun J, Xu Z, Zhang Z, Zhou Q, Xu J, Chen H, Wang C, Ouyang J.
Institution: Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
Abstract: Objective: To develop and externally validate a novel nomogram in biopsy-naïve patients with prostate-specific antigen (PSA) <10 ng/ml and PI-RADS v2.1 = 3 lesions.
Methods: We retrospectively collected 307 men that underwent initial biopsy from October 2015 to January 2022 in Cohort 1 (The First Affiliated Hospital of Soochow University). External cohort (Cohort 2, Kunshan Hospital) included 109 men that met our criteria from July 2016 to June 2021. By 3D Slicer Software, the volume of all lesions was divided into two subgroups (PI-RADS v2.1 = 3a and 3b). Logistic regression analysis was performed to screen for variables and construct nomogram by analyzing clinical data from Cohort 1. Receiver operating characteristics curve analysis, calibration plot and decision curve analysis (DCA) were plotted to validate the nomogram in external cohort.
Results: A total of 70 (22.8%) patients was diagnosed with prostate cancer in Institution 1. Among them, 34 (11.1%) had clinically significant prostate cancer (csPCa). Age, prostate-specific antigen density, digital rectal examination, PI-RADS v2.1 = 3 subgroups (3a and 3b) and apparent diffusion coefficient (ADC, <750 mm2 /s) were predictive factors for prostate cancer (PCa) and csPCa. High area under the curve of the nomogram was found in Cohort 1 and Cohort 2 for PCa (0.857 vs. 0.850) and for csPCa (0.896 vs. 0.893). Calibration curves showed excellent agreement between the predicted probability and actual risk for the models in internal and external validation. The DCA demonstrated net benefit of our nomogram.
Conclusion: Until now, this is the first nomogram that predicts PCa and csPCa in biopsy-naïve patients with PSA <10 ng/ml and PI-RADS v2.1 = 3 lesions. Furthermore, PI-RADS v2.1 = 3 subgroups were considered to be an independent risk factor in our model. Our nomogram may assist urologists in biopsy decision making for these so-called "double gray zone" patients.
A Three-Dimensionally Printed Otological Model for Cholesteatoma Mastoidectomy Training
Authors: de Souza MA, Bento RF, Lopes PT.
Institution: Otolaryngology Department, University of São Paulo School of Medicine, São Paulo, Brazil.
Abstract: purpose: To relate the creation and expert validation (face and content validity) of an affordable three-dimensional (3D) printed model of temporal bones with chronic otitis media with cholesteatoma (COMC) as a simulator for mastoidectomy.
Methods: We performed computed tomography (CT) of the temporal bones of a patient with COMC followed at the University of São Paulo (USP) Hospital with 3D Slicer to create a 3-D model of the affected bone using light-curing resin and silicone (cholesteatoma). The final 3-D printed images were scored by 10 otologists using a customized version of the Michigan Standard Simulation Scale Experience (MiSSES). Internal consistency and inter-rater reliability were assessed using Cronbach's α and intraclass correlations.
Results: Otologists consistently scored the model positively for fidelity, educational value, reactions, and the overall model quality. Nine otologists agreed that the model was a good educational device for surgical training of COMC. All experts deemed the model ready-or nearly ready-for use. The final cost of the model, including raw materials and manufacturing, was 120 USD.
Conclusions: Using 3D printing technology, we created the first anatomically accurate, low-cost, disease-reproducing 3D model of temporal bones for mastoidectomy training for cholesteatoma.
Authors: Sareen K.
Institution: Sant Parmanand Hospital, New Delhi, India.
Abstract: Background: Computed Tomography (CT) scanning offers an accurate structural definition of bones, blood vessels, and soft tissues; however, mental integration of cross-sectional 2D CT images for a 3D understanding of complex anatomical structures becomes difficult when the field of view is confined to the temporal bone. This project tried to provide a feasible solution to this problem by creating a navigable 3D virtual model which may aid in better comprehension of the temporal bone anatomy.
Methods: A helical-CT scan was used to obtain high-resolution cross-sectional slices of a cadaveric human temporal bone. Using the volume-rendering capabilities of 3D Slicer, which involves volume data management, cropping of the data set, and threshold painting, detailed anatomical structures were segmented based on the intensity captured from different regions. This volumetric data was converted to an interactive virtual model using Blender®.
Results: The final product is a web page that allows interaction and navigation with a 3D annotated model of the temporal bone, which can be accessed from any device with a web browser.
Conclusion: This model can function as a training tool for students, teachers, and practitioners to understand and review the complex anatomy of the temporal bone.
Maxillary Antral Pseudocyst Drift after Osteotome Sinus Floor Elevation with Simultaneous Implant Placement: A Case Report and Literature Review
Authors: Wang P, Huang N, Ren J, Gong P, Long J, Huang B.
Institution: West China School of Stomatology, Sichuan University, Chengdu, China.
Abstract: This report describes maxillary antral pseudocyst drift after maxillary sinus floor augmentation through osteotome sinus floor elevation with simultaneous implant placement. 3D Slicer was used to measure the pseudocyst and maxilla for the placement of the implants; follow-up visits were scheduled at 6, 12, and 22 months. No adverse effects were observed during or after surgery, and all implants exhibited osseointegration without mobility. At 6 months after surgery, the pseudocyst had moved posterolaterally from the preoperative position near the anterior medial maxillary sinus, then returned to its original position at 12 months. However, it had remigrated to the posterolateral position at 22 months. The preoperative volume of the pseudocyst was 3.795 mm3; it was 2.370, 3.439, and 2.930 mm3 at 6, 12, and 22 months after surgery, respectively. The changes in pseudocyst drift and volume did not have a substantial negative influence on the implants, presumably because of cystic attachment and the recurrence of multiple pseudocysts at different locations. The risks associated with changes in a pseudocyst can be avoided, if an appropriate treatment plan is selected.
Radiomic Analysis Based on Magnetic Resonance Imaging for Predicting PD-L2 Expression in Hepatocellular Carcinoma
Publication: Cancers (Basel). 2023 Jan 5;15(2):365. PMID: 36672315 | PDF
Authors: Tao YY, Shi Y, Gong XQ, Li L, Li ZM, Yang L, Zhang XM.
Institution: Medical Imaging Key Laboratory of Sichuan Province, Interventional Medical Center, Department of Radiology, Medical Research Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
Abstract: Hepatocellular carcinoma (HCC) is the sixth most common malignant tumour and the third leading cause of cancer death in the world. The emerging field of radiomics involves extracting many clinical image features that cannot be recognized by the human eye to provide information for precise treatment decision making. Radiomics has shown its importance in HCC identification, histological grading, microvascular invasion (MVI) status, treatment response, and prognosis, but there is no report on the preoperative prediction of programmed death ligand-2 (PD-L2) expression in HCC. The purpose of this study was to investigate the value of MRI radiomic features for the non-invasive prediction of immunotherapy target PD-L2 expression in hepatocellular carcinoma (HCC). A total of 108 patients with HCC confirmed by pathology were retrospectively analysed. Immunohistochemical analysis was used to evaluate the expression level of PD-L2. 3D Slicer software was used to manually delineate volumes of interest (VOIs) and extract radiomic features on preoperative T2-weighted, arterial-phase, and portal venous-phase MR images. Least absolute shrinkage and selection operator (LASSO) was performed to find the best radiomic features. Multivariable logistic regression models were constructed and validated using fivefold cross-validation. The area under the receiver characteristic curve (AUC) was used to evaluate the predictive performance of each model. The results show that among the 108 cases of HCC, 50 cases had high PD-L2 expression, and 58 cases had low PD-L2 expression. Radiomic features correlated with PD-L2 expression. The T2-weighted, arterial-phase, and portal venous-phase and combined MRI radiomics models showed AUCs of 0.789 (95% CI: 0.702-0.875), 0.727 (95% CI: 0.632-0.823), 0.770 (95% CI: 0.682-0.875), and 0.871 (95% CI: 0.803-0.939), respectively. The combined model showed the best performance. The results of this study suggest that prediction based on the radiomic characteristics of MRI could noninvasively predict the expression of PD-L2 in HCC before surgery and provide a reference for the selection of immune checkpoint blockade therapy.
Correlation Between Unilateral Internal Carotid Artery Stenosis and Asymmetric Distribution of Enlarged Perivascular Spaces in Patients With Acute Cerebral Infarction
Authors: Jian XL, Zhang M, Yun WW.
Abstract: Objective: To explore the correlation between unilateral internal carotid artery (ICA) stenosis and asymmetrical distribution of enlarged perivascular spaces (EPVS) in patients with acute cerebral infarction.
Methods: Acute cerebral infarction patients with unilateral ICA stenosis hospitalized in Changzhou Second People's Hospital from October 2020 to December 2021 were collected. Routine cranial MRI and CT angiography were completed for each patient. The 3D Slicer software was used to quantitatively analyze the volume of patient's EPVS. Patients were divided into moderate stenosis group and severe stenosis/occlusion group according to the degree of ICA stenosis. Baseline data were compared between the two groups. Patients were further divided into three groups: moderate stenosis, severe stenosis and occlusion groups, and the ipsilateral and contralateral EPVS volume of ICA stenosis patients was compared. The asymmetry index (AI) was calculated for EPVS in the basal ganglia region (BG-EPVS) and EPVS in the centrum semiovale (CSO-EPVS). Patients with AI≥0.2 were included in the EPVS asymmetry group, while the rest were in the EPVS symmetry group, and the degree of unilateral ICA stenosis was compared between the two groups. Multivariate logistic regression model was used to analyze the relationship between ICA severe stenosis/occlusion and the asymmetric distribution of BG-EPVS.
Results: A total of 122 patients (96 males and 26 females) were enrolled, aged (70±10) years, with 81 cases in the unilateral ICA severe stenosis/occlusion group (46 cases of severe stenosis and 35 of occlusion) and 41 cases in the moderate stenosis group. Patients in the unilateral ICA severe stenosis/occlusion group had greater BG-EPVS volume [(4.08±0.76) mm3]and proportion of asymmetric distribution of BG-EPVS [75.3%(61/81)] than those of the moderate stenosis group [(3.12±0.85) mm3 and 39.0% (16/41)], with statistically significant differences (both P<0.001). The BG-EPVS volumes of the ipsilateral side of the stenosis in the severe stenosis group and the occlusion group [(3.34±0.86) mm3 and (3.93±0.60) mm3] were significantly greater than those of the contralateral side [(2.65±1.28) mm3 and (3.21±0.88) mm3], with statistically significant differences (both P<0.001). Correlation analysis indicated that the degree of unilateral ICA stenosis was positively correlated with the BG-EPVS volume on the stenosis side (r=0.62, P<0.001). Further comparison of the degree of unilateral ICA stenosis between the EPVS symmetric and asymmetric groups showed that the proportion of unilateral ICA severe stenosis/occlusion in the BG-EPVS asymmetry group was higher than that in the symmetric group [79.2%(61/77) vs 44.4%(20/45),P<0.001]. Multivariate logistic regression analysis showed that unilateral ICA severe stenosis/occlusion (OR=4.280, 95%CI: 1.743-10.508, P =0.002) and age (OR=1.055, 95%CI: 1.001-1.112, P=0.044) were risk factors for asymmetric distribution of BG-EPVS.
Conclusions: The severe stenosis/occlusion of the unilateral ICA and age are the risk factors for the asymmetric distribution of the BG-EPVS in patients with acute cerebral infarction. The ipsilateral EPVS volume of unilateral ICA stenosis is larger than that of the contralateral side, and the degree of ICA stenosis is positively correlated with the severity of BG-EPVS.
Radiomics to Predict the Mortality of Patients With Rheumatoid Arthritis-Associated Interstitial Lung Disease: A Proof-of-Concept Study
Publication: Front Med (Lausanne). 2023 Jan 9;9:1069486. PMID: 36698825 | PDF
Authors: Venerito V, Manfredi A, Lopalco G, Lavista M, Cassone G, Scardapane A, Sebastiani M, Iannone F.
Institution: Rheumatology Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.
Abstract: Objectives: Patients with rheumatoid arthritis (RA) and interstitial lung disease (ILD) have increased mortality compared to the general population and factors capable of predicting RA-ILD long-term clinical outcomes are lacking. In oncology, radiomics allows the quantification of tumour phenotype by analysing the characteristics of medical images. Using specific software, it is possible to segment organs on high-resolution computed tomography (HRCT) images and extract many features that may uncover disease characteristics that are not detected by the naked eye. We aimed to investigate whether features from whole lung radiomic analysis of HRCT may alone predict mortality in RA-ILD patients.
Methods: High-resolution computed tomographies of RA patients from January 2012 to March 2022 were analyzed. The time between the first available HRCT and the last follow-up visit or ILD-related death was recorded. We performed a volumetric analysis in 3D Slicer, automatically segmenting the whole lungs and trachea via the Lung CT Analyzer. A LASSO-Cox model was carried out by considering ILD-related death as the outcome variable and extracting radiomic features as exposure variables.
Results: We retrieved the HRCTs of 30 RA-ILD patients. The median survival time (interquartile range) was 48 months (36-120 months). Thirteen out of 30 (43.33%) patients died during the observation period. Whole line segmentation was fast and reliable. The model included either the median grey level intensity within the whole lung segmentation [high-resolution (HR) 9.35, 95% CI 1.56-55.86] as a positive predictor of death and the 10th percentile of the number of included voxels (HR 0.20, 95% CI 0.05-0.84), the voxel-based pre-processing information (HR 0.23, 95% CI 0.06-0.82) and the flatness (HR 0.42, 95% CI 0.18-0.98), negatively correlating to mortality. The correlation of grey level values to their respective voxels (HR 1.52 95% CI 0.82-2.83) was also retained as a confounder.
Conclusion: Radiomic analysis may predict RA-ILD patients' mortality and may promote HRCT as a digital biomarker regardless of the clinical characteristics of the disease.
Evaluation of the Prognosis of Acute Subdural Hematoma According to the Density Differences Between Gray and White Matter
Publication: Front Neurol. 2023 Jan 6;13:1024018. PMID: 36686517 | PDF
Authors: Li Z, Feng Y, Wang P, Han S, Zhang K, Zhang C, Lu S, Lv C, Zhu F, Bie L.
Institution: Department of Neurosurgery of the First Clinical Hospital, Jilin University, Changchun, China.
Abstract: Objective: Acute subdural hematoma (ASDH) is a common neurological emergency, and its appearance on head-computed tomographic (CT) imaging helps guide clinical treatment. To provide a basis for clinical decision-making, we analyzed that the density difference between the gray and white matter of the CT image is associated with the prognosis of patients with ASDH.
Methods: We analyzed the data of 194 patients who had ASDH as a result of closed traumatic brain injury (TBI) between 2018 and 2021. The patients were subdivided into surgical and non-surgical groups, and the non-surgical group was further subdivided into "diffused [hematoma]" and "non-diffused" groups. The control group's CT scans were normal. The 3D Slicer software was used to quantitatively analyze the density of gray and white matter depicted in the CT images.
Results: Imaging evaluation showed that the median difference in density between the gray and white matter on the injured side was 4.12 HU (IQR, 3.91-4.22 HU; p < 0.001) and on the non-injured side was 4.07 HU (IQR, 3.90-4.19 HU; p < 0.001), and the hematoma needs to be surgically removed. The median density difference value of the gray and white matter on the injured side was 3.74 HU (IQR, 3.53-4.01 HU; p < 0.001) and on the non-injured side was 3.71 HU (IQR, 3.69-3.73 HU; p < 0.001), and the hematoma could diffuse in a short time.
Conclusion: Quantitative analysis of the density differences in the gray and white matter of the CT images can be used to evaluate the clinical prognosis of patients with ASDH.
The Knosp Criteria Revisited: 3-Dimensional Volumetric Analysis as a Predictive Tool for Extent of Resection in Complex Endoscopic Pituitary Surgery
Authors: DiRisio AC, Feng R, Shuman WH, Platt S, Price G, Dullea JT, Gilja S, D'Andrea MR, Delman BN, Bederson JB, Shrivastava RK.
Institution: Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Abstract: Background: The Knosp criteria have been the historical standard for predicting cavernous sinus invasion, and therefore extent of surgical resection, of pituitary macroadenomas. Few studies have sought to reappraise the utility of this tool after recent advances in visualization and modeling of tumors in complex endoscopic surgery.
Objective: To evaluate our proposed alternative method, using 3-dimensional (3D) volumetric imaging, and whether it can better predict extent of resection in nonfunctional pituitary adenomas.
Methods: Patients who underwent endoscopic transsphenoidal resection of pituitary macroadenomas at our institution were reviewed. Information was collected on neurological, endocrine, and visual function. Volumetric segmentation was performed using 3D Slicer software. Relationship of tumor volume, clinical features, and Knosp grade on extent of resection was examined.
Results: One hundred forty patients were identified who had transsphenoidal resection of nonfunctional pituitary adenomas. Macroadenomas had a median volume of 6 cm3 (IQR 3.4-8.7), and 17% had a unilateral Knosp grade of at least 3B. On multiple logistic regression, only smaller log-transformed preoperative tumor volume was independently associated with increased odds of gross total resection (GTR; odds ratio: 0.27, 95% CI: 0.07-0.89, P < .05) when controlling for tumor proliferative status, age, and sex (area under the curve 0.67). The Knosp criteria did not independently predict GTR in this cohort (P > .05, area under the curve 0.46).
Conclusion: Increasing use of volumetric 3D imaging may better anticipate extent of resection compared with the Knosp grade metric and may have a greater positive predictive value for GTR. More research is needed to validate these findings and implement them using automated methods.
Differentiation of Lung Metastases Originated From Different Primary Tumors Using Radiomics Features Based on CT Imaging
Publication: Acad Radiol. 2023 Jan;30(1):40-6. PMID: 35577699
Authors: Shang H, Li J, Jiao T, Fang C, Li K, Yin D, Zeng Q.
Institution: Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, No. 16766 Jingshi Road, Jinan, Shandong, China.
Abstract: Rationale and objectives: To explore the feasibility of differentiating three predominant metastatic tumor types using lung computed tomography (CT) radiomics features based on supervised machine learning.
Materials and Methods: This retrospective analysis included 252 lung metastases (LM) (from 78 patients), which were divided into the training (n = 176) and test (n = 76) cohort randomly. The metastases originated from colorectal cancer (n = 97), breast cancer (n = 87), and renal carcinoma (n = 68). An additional 77 LM (from 35 patients) were used for external validation. All radiomics features were extracted from lung CT using an open-source software, 3D Slicer. The least absolute shrinkage and selection operator (LASSO) method selected the optimal radiomics features to build the model. Random forest and support vector machine (SVM) were selected to build three-class and two-class models. The performance of the classification model was evaluated with the area under the receiver operating characteristic curve (AUC) by two strategies: one-versus-rest and one-versus-one.
Results: Eight hundred and fifty-one quantitative radiomics features were extracted from lung CT. By LASSO, 23 optimal features were extracted in three-class, and 25, 29, and 35 features in two-class for differentiating every two of three LM (colorectal cancer vs. renal carcinoma, colorectal cancer vs. breast cancer, and breast cancer vs. renal carcinoma, respectively). The AUCs of the three-class model were 0.83 for colorectal cancer, 0.79 for breast cancer, and 0.91 for renal carcinoma in the test cohort. In the external validation cohort, the AUCs were 0.77, 0.83, and 0.81, respectively. Swarmplot shows the distribution of radiomics features among three different LM types. In the two-class model, high accuracy and AUC were obtained by SVM. The AUC of discriminating colorectal cancer LM from renal carcinoma LM was 0.84, and breast cancer LM from colorectal cancer LM and renal carcinoma LM were 0.80 and 0.94, respectively. The AUCs were 0.77, 0.78, and 0.84 in the external validation cohort.
Conclusion: Quantitative radiomics features based on Lung CT exhibited good discriminative performance in LM of primary colorectal cancer, breast cancer, and renal carcinoma.
MRI Radiomic Features of Peritumoral Edema May Predict the Recurrence Sites of Glioblastoma Multiforme
Publication: Front Oncol. 2023 Jan 4;12:1042498. PMID: 36686829 | PDF
Authors: Long H, Zhang P, Bi Y, Yang C, Wu M, He D, Huang S, Yang K, Qi S, Wang J.
Institution: Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Background and Purpose: As one of the most aggressive malignant tumor in the central nervous system, the main cause of poor outcome of glioblastoma (GBM) is recurrence, a non-invasive method which can predict the area of recurrence pre-operation is necessary.To investigate whether there is radiological heterogeneity within peritumoral edema and identify the reproducible radiomic features predictive of the sites of recurrence of glioblastoma(GBM), which may be of value to optimize patients' management.
Materials and Methods: The clinical information and MR images (contrast-enhanced T1 weighted and FLAIR sequences) of 22 patients who have been histologically proven glioblastoma, were retrospectively evaluated. Kaplan-Meier methods was used for survival analysis. Oedematous regions were manually segmented by an expert into recurrence region, non-recurrence region. A set of 94 radiomic features were obtained from each region using the function of analyzing MR image of 3D Slicer. Paired t test was performed to identify the features existing significant difference. Subsequently, the data of two patients from TCGA database was used to evaluate whether these features have clinical value.
Results: Ten features with significant differences between the recurrence and non-recurrence subregions were identified and verified on two individual patients from the TCGA database with pathologically confirmed diagnosis of GBM.
Conclusions: Our results suggested that heterogeneity does exist in peritumoral edema, indicating that the radiomic features of peritumoral edema from routine MR images can be utilized to predict the sites of GBM recurrence. Our findings may further guide the surgical treatment strategy for GBM.
Clinical Study on Application of 3D Slicer Software Assisted Domestic Frameless Stereotactic Robot in Biopsy of Intracranial Lesions
Authors: Chen H, Yan X, He F, Ding SC, Diao JF, Guo H, Cao SM, Yang CJ, Yin F.
Institution: Department of Neurosurgery, Aerospace Central Hospital, Beijing, China.
Abstract: Objective: To examine the application value of 3D Slicer software assisted domestic frameless stereotactic robot in biopsy of intracranial lesions.
Methods: A retrospective analysis was performed on 80 patients who admitted consecutively and underwent intracerebral lesions biopsy with the domestic frameless stereotactic robot at Department of Neurosurgery, Aerospace Central Hospital from January 2019 to December 2021. There were 36 males and 44 females, with a mean age of (38.5±18.0) years (range: 6 to 71 years). Before surgery only enhanced T1-weighted three-dimensional magnetization prepared gradient echo sequences and diffusion tensor imaging scans were performed. Self-reconstruction of intracranial lesions, cerebral cortex and blood vessels was carried out using 3D Slicer software system after the DICOM format imaging data of 80 patients were collected. These imaging data were merged to the workstation of the domestic frameless stereotactic robot for preoperative surgical planning and the surgical puncture path was designed to avoid blood vessels in the brain functional area, cerebral cortex and sulcus.
Results: All frameless stereotactic biopsy were successfully performed. Postoperative pathological diagnosis included 50 cases of diffuse astrocytic and oligodendroglioma, 15 cases of lymphoma, 5 cases of metastatic tumors, 5 cases of inflammatory demyelinating disease, 2 cases of inflammatory granuloma, 1 case of hemangioma, 1 case of acute lymphoblastic leukemia intracranial invasion and 1 case of seminoma. The positive diagnosis rate was 100% (80/80). Postoperative imaging confirmed that the puncture path and target were accurately implemented according to the preoperative planning, and the target error was (1.32±0.44) mm (range: 0.55 to 1.99 mm). One case of puncture-related bleeding occurred at the target after surgery and improved after treatment.
Conclusion: The three-dimensional multimodal images reconstructed by the 3D Slicer software before operation could help the surgeons make the preoperative planning and reduce the risk of stereotactic brain biopsy.
Liver Cirrhosis and Tumor Location Can Affect the Range of Intrahepatic Microwave Ablation Zone
Publication: Int J Hyperthermia. 2023;40(1):2181843. PMID: 36854449 | PDF
Authors: Ding WZ, Wei H, Wu JP, Cheng ZG, Han ZY, Liu FY, Yu J, Liang P.
Institution: Fifth Medical Center of Chinese, PLA General Hospital, Beijing, China.
Abstract: Background: The range of an ablation zone (AZ) plays a crucial role in the treatment effect of microwave ablation (MWA). The aim of this study was to analyze the factors influencing the AZ range.
Methods: Fourteen factors in four areas were included: patient-related factors (sex, age), disease-related factors (tumor location, liver cirrhosis), serological factors (ALT, AST, total protein, albumin, total bilirubin, direct bilirubin, and platelets), and MWA parameters (ablation time, power, and needle type). Multiple sequence MRI was used to delineate AZ by three radiologists using 3D Slicer. MATLAB was used to calculate the AZ length, width, and area of the largest section. Linear regression analysis was used to analyze influencing factors. Moreover, a subgroup analysis was conducted for patients with viral hepatitis.
Result: 220 patients with 290 tumors were included between 2010-2021. In addition to MWA parameters, cirrhosis and tumor location were significant factors that influenced AZ (p < 0.001). The standardized coefficient (beta) of cirrhosis (cirrhosis vs. non-cirrhosis) was positive, which meant cirrhosis would lead to a decrease in AZ range. The beta of tumor location (near the hepatic hilar zone, intermediate zone, and periphery zone) was negative, indicating that AZ range decreased as the tumor location approached the hepatic hilum. For viral hepatitis patients, Fibrosis 4 (FIB4) score was a significant factor influencing AZ (p < 0.001), and the beta was negative, indicating that AZ range decreased as FIB4 increased.
Conclusion: Liver cirrhosis, tumor location, and FIB4 affect the AZ range and should be considered when planning MWA parameters.
A Magnetic Resonance Imaging Based Radiomics Model to Predict Mitosis Cycles in Intracranial Meningioma
Authors:Krähling H, Musigmann M, Akkurt BH, Sartoretti T, Sartoretti E, Henssen DJHA, Stummer W, Heindel W, Brokinkel B, Mannil M.
Institution: University Clinic for Radiology, University Hospital Muenster, Westfälische Wilhelms-University Muenster, Muenster, Germany.
Abstract: The aim of this study was to develop a magnetic resonance imaging (MRI) based radiomics model to predict mitosis cycles in intracranial meningioma grading prior to surgery. Preoperative contrast-enhanced T1-weighted (T1CE) cerebral MRI data of 167 meningioma patients between 2015 and 2020 were obtained, preprocessed and segmented using the 3D Slicer software and the PyRadiomics plugin. In total 145 radiomics features of the T1CE MRI images were computed. The criterion on the basis of which the feature selection was made is whether the number of mitoses per 10 high power field (HPF) is greater than or equal to zero. Our analyses show that machine learning algorithms can be used to make accurate predictions about whether the number of mitoses per 10 HPF is greater than or equal to zero. We obtained our best model using Ridge regression for feature pre-selection, followed by stepwise logistic regression for final model construction. Using independent test data, this model resulted in an AUC (Area under the Curve) of 0.8523, an accuracy of 0.7941, a sensitivity of 0.8182, a specificity of 0.7500 and a Cohen's Kappa of 0.5576. We analyzed the performance of this model as a function of the number of mitoses per 10 HPF. The model performs well for cases with zero mitoses as well as for cases with more than one mitosis per 10 HPF. The worst model performance (accuracy = 0.6250) is obtained for cases with one mitosis per 10 HPF. Our results show that MRI-based radiomics may be a promising approach to predict the mitosis cycles in intracranial meningioma prior to surgery. Specifically, our approach may offer a non-invasive means of detecting the early stages of a malignant process in meningiomas prior to the onset of clinical symptoms.
Advantages of a Training Course for Surgical Planning in Virtual Reality for Oral and Maxillofacial Surgery: Crossover Study
Publication: JMIR Serious Games. 2023 Jan 19;11:e40541. PMID: 36656632 | PDF
Authors: Ulbrich M, Van den Bosch V, Bönsch A, Gruber LJ, Ooms M, Melchior C, Motmaen I, Wilpert C, Rashad A, Kuhlen TW, Hölzle F, Puladi B.
Institution: Department of Oral and Maxillofacial Surgery, University Hospital RWTH Aachen, Aachen, Germany.
Abstract: Background: As an integral part of computer-assisted surgery, virtual surgical planning (VSP) leads to significantly better surgery results, such as for oral and maxillofacial reconstruction with microvascular grafts of the fibula or iliac crest. It is performed on a 2D computer desktop screen (DS) based on preoperative medical imaging. However, in this environment, VSP is associated with shortcomings, such as a time-consuming planning process and the requirement of a learning process. Therefore, a virtual reality (VR)-based VSP application has great potential to reduce or even overcome these shortcomings due to the benefits of visuospatial vision, bimanual interaction, and full immersion. However, the efficacy of such a VR environment has not yet been investigated.
Objective: This study aimed to demonstrate the possible advantages of a VR environment through a substep of VSP, specifically the segmentation of the fibula (calf bone) and os coxae (hip bone), by conducting a training course in both DS and VR environments and comparing the results.
Methods: During the training course, 6 novices were taught how to use a software application in a DS environment, 3D Slicer) and in a VR environment (Elucis) for the segmentation of the fibula and os coxae, and they were asked to carry out the maneuvers as accurately and quickly as possible. Overall, 13 fibula and 13 os coxae were segmented for each participant in both methods (VR and DS), resulting in 156 different models (78 fibula and 78 os coxae) per method (VR and DS) and 312 models in total. The individual learning processes in both environments were compared using objective criteria (time and segmentation performance) and self-reported questionnaires. The models resulting from the segmentation were compared mathematically (Hausdorff distance and Dice coefficient) and evaluated by 2 experienced radiologists in a blinded manner.
Results: A much faster learning curve was observed for the VR environment than the DS environment (β=.86 vs β=.25). This nearly doubled the segmentation speed (cm3/min) by the end of training, leading to a shorter time (P<.001) to reach a qualitative result. However, there was no qualitative difference between the models for VR and DS (P=.99). The VR environment was perceived by participants as more intuitive and less exhausting, and was favored over the DS environment.
Conclusions: The more rapid learning process and the ability to work faster in the VR environment could save time and reduce the VSP workload, providing certain advantages over the DS environment.
Lesion Size and Long-Term Cognitive Outcome After Pediatric Stroke: A Comparison Between Two Techniques to Assess Lesion Size
Authors: Everts R, Bertato S, Steinlin M, Slavova N, Grunt S, Steiner L.
Institution: Division of Neuropediatrics, Development and Rehabilitation, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
Abstract: Background: There is little consensus on how lesion size impacts long-term cognitive outcome after pediatric arterial ischemic stroke (AIS). This study, therefore, compared two techniques to assessed lesion size in the chronic phase after AIS and determined their measurement agreement in relation to cognitive functions in patients after pediatric stroke.
Methods: Twenty-five patients after pediatric AIS were examined in the chronic phase (>2 years after stroke) in respect to intelligence, memory, executive functions, visuo-motor functions, motor abilities, and disease-specific outcome. Lesion size was measured using the ABC/2 formula and segmentation technique (3D Slicer). Correlation analysis determined the association between volumetry techniques and outcome measures in respect to long-term cognitive outcome.
Results: The measurements from the ABC/2 and segmentation technique were strongly correlated (r = 0.878, p < .001) and displayed agreement in particular for small lesions. Lesion size from both techniques was significantly correlated with disease-specific outcome (p < .001) and processing speed (p < .005) after controlling for age at stroke and multiple comparison.
Conclusion: The two techniques showed convergent validity and were both significantly correlated with long-term outcome after pediatric AIS. Compared to the time-consuming segmentation technique, ABC/2 facilitates clinical and research work as it requires relatively little time and is easy to apply.
Association Between Emphysema and Other Pulmonary Computed Tomography Patterns in COVID-19 Pneumonia
Publication: J Med Virol. 2023 Jan;95(1):e28293. PMID: 36358023 | PDF
Authors: Han K, Wang J, Zou Y, Zhang Y, Zhou L, Yin Y.
Institution: Fetal-Neonatal Neuroimaging and Developmental Science Center, Division of Newborn Medicine, Boston Children's Hospital, Boston, USA.
Abstract: To evaluate the chest computed tomography (CT) findings of patients with Corona Virus Disease 2019 (COVID-19) on admission to hospital. And then correlate CT pulmonary infiltrates involvement with the findings of emphysema. We analyzed the different infiltrates of COVID-19 pneumonia using emphysema as the grade of pneumonia. We applied open-source assisted software, 3D Slicer to model the lungs and lesions of 66 patients with COVID-19, which were retrospectively included. we divided the 66 COVID-19 patients into the following two groups: (A) 12 patients with less than 10% emphysema in the low-attenuation area less than -950 Hounsfield units (%LAA-950), (B) 54 patients with greater than or equal to 10% emphysema in %LAA-950. Imaging findings were assessed retrospectively by two authors and then pulmonary infiltrates and emphysema volumes were measured on CT using 3D Slicer software. Differences between pulmonary infiltrates, emphysema, Collapsed, affected of patients with CT findings were assessed by Kruskal-Wallis and Wilcoxon test, respectively. Statistical significance was set at p < 0.05. The left lung (A) affected left lung 20.00/affected right lung 18.50, (B) affected left lung 13.00/affected right lung 11.50 was most frequently involved region in COVID-19. In addition, collapsed left lung, (A) collapsed left lung 4.95/collapsed right lung 4.65, (B) collapsed left lung 3.65/collapsed right lung 3.15 was also more severe than the right one. There were significant differences between the Group A and Group B in terms of the percentage of CT involvement in each lung region (p < 0.05), except for the inflated affected total lung (p = 0.152). The median percentage of collapsed left lung in the Group A was 20.00 (14.00-30.00), right lung was 18.50 (13.00-30.25) and the total was 19.00 (13.00-30.00), while the median percentage of collapsed left lung in the Group B was 13.00 (10.00-14.75), right lung was 11.50 (10.00-15.00) and the total was 12.50 (10.00-15.00). The percentage of affected left lung is an independent predictor of emphysema in COVID-19 patients. We need to focus on the left lung of the patient as it is more affected. The people with lower levels of emphysema may have more collapsed segments. The more collapsed segments may lead to more serious clinical feature.
A High-Resolution Pediatric Female Whole-Body Numerical Model With Comparison to a Male Model
Publication: Phys Med Biol. 2023 Jan 13;68(2). PMID: 36595234
Authors: Ntolkeras G, Jeong H, Zöllei L, Dmytriw AA, Purvaziri A, Lev MH, Grant PE, Bonmassar G.
Institution: Fetal-Neonatal Neuroimaging and Developmental Science Center, Division of Newborn Medicine, Boston Children's Hospital, Boston, USA.
Abstract: Objective: Numerical models are central in designing and testing novel medical devices and in studying how different anatomical changes may affect physiology. Despite the numerous adult models available, there are only a few whole-body pediatric numerical models with significant limitations. In addition, there is a limited representation of both male and female biological sexes in the available pediatric models despite the fact that sex significantly affects body development, especially in a highly dynamic population. As a result, we developed Athena, a realistic female whole-body pediatric numerical model with high-resolution and anatomical detail.
Approach: We segmented different body tissues through Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) images of a healthy 3.5 year-old female child using 3D Slicer. We validated the high anatomical accuracy segmentation through two experienced sub-specialty-certified neuro-radiologists and the inter and intra-operator variability of the segmentation results comparing sex differences in organ metrics with physiologic values. Finally, we compared Athena with Martin, a similar male model, showing differences in anatomy, organ metrics, and MRI dosimetric exposure.
Main results:We segmented 267 tissue compartments, which included 50 brain tissue labels. The tissue metrics of Athena displayed no deviation from the literature value of healthy children. We show the variability of brain metrics in the male and female models. Finally, we offer an example of computing Specific Absorption Rate and Joule heating in a toddler/preschooler at 7T MRI.
Significance: This study introduces a female realistic high-resolution numerical model using MRI and CT scans of a 3.5 year-old female child, the use of which includes but is not limited to radiofrequency safety studies for medical devices (e.g. an implantable medical device safety in MRI), neurostimulation studies, and radiation dosimetry studies. This model will be open source and available on the Athinoula A. Martinos Center for Biomedical Imaging website.
Anatomical Morphology and Related Angles of Foramen Ovale: A Three-dimensional Computed Tomography Reconstruction
Authors: Cheng Z, Hu YL, Sun YX, Liang LZ, Pan DD, Wang DW.
Institution: Department of Neurosurgery, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China.
Abstract: This study aimed to report the three-dimensional reconstruction of the foramen ovale (FO) based on computed tomography angiography and describe its shape and related angles. A retrospective analysis of 199 adult patients who were hospitalised at the Department of Neurosurgery, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, China, from January to December 2020 was conducted. The original DICOM files of patients' computed tomography scans were processed by 3D Slicer software to reconstruct the three-dimensional skull. The morphological characteristics of the FO on both sides were analysed. Their size, related angles and volumes, and the differences between the two sides and gender were compared. A total of 398 FO from 199 patients were studied. The most frequent shape of the FO was oval, accounting for 54.27%. The mean lengths of the right and the left sides were 5.40±1.51 and 5.10±1.18mm, respectively. The mean width on the right and left sides was 3.23±1.16 and 3.33±1.19 mm, respectively. The FO is most commonly oval in shape. Clinicians may use the anatomical characteristics regarding the size and shape of the FO for diagnosis and treatment.