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

1,467,466+ downloads in the last 11 years (269,677 in 2023, 206,541 in 2022)
over 17.900+ literature search results on Google Scholar

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.

2023

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

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

Publication: IEEE Trans Ultrason Ferroelectr Freq Control. 2023 Jul;70(7):587-99. PMID: 37155375

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

Publication: Otolaryngol Head Neck Surg. 2023 Jul;169(1):151-156. PMID: 36939460

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.

Multimodal Measurements of Levator Bowl Volume in Nulligravid Asymptomatic Women: Endovaginal Ultrasound Versus MRI

Publication: Int Urogynecol J. 2023 Jul;34(7):1627-33. PMID: 36656345

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.

The Traction Force of the Pulled Limb in Hip Arthroscopic Surgery Is Determined by Stiffness Coefficient Which Is Significantly Related to Muscle Volume

Publication: Knee Surg Sports Traumatol Arthrosc. 2023 Jul;31(7):2708-2715. PMID: 36477348

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

Publication: Int Urogynecol J. 2023 Jul;34(7):1627-33. PMID: 36656345

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

Publication: J Musculoskelet Neuronal Interact. 2023 Jun 1;23(2):196-204. PMID: 37259659 | PDF

Authors: Tekin ZN, Dogruoz Karatekin B, Dogan MB, Bilgi Z.

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

Publication: Clin Neurol Neurosurg. 2023 Jun;229:107730. PMID: 37086587

Authors: Tian Q, Yi J, Wu Y, Wang S, Qu Y, Cai Q.

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

Publication: IEEE Trans Biomed Eng. 2023 Jun;70(6):1902-10. PMID: 37015676

Authors: Perera-Bel E, Aycock KN, Salameh ZS, Gomez-Barea M, Davalos RV, Ivorra A, Ballester MAG.

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

Publication: Oral Maxillofac Surg. 2023 Jun;27(2):269-281. PMID: 35426586

Authors: Carvalho FSR, Soares ECS, de Medeiros JR, Júnior JMM, Hyppolito JOP, de Barros Silva PG, Ribeiro TR, Costa FWG.

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.

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

Authors: Han T, Jiang S, Xiong J, Cui J, Shen W.

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.

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

Publication: Heliyon. 2023 May 18;9(6):e16193. PMID: 37251467 | PDF

Authors: Zhou L, Ren Y, Li Z, Zhang H, Wei H, Song P, Cheng L, Wang W, Gao L, Lei P, Hua Q, Chen Q, Zhou J, Li G, Cai Q.

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.

Laser Interstitial Thermal Therapy in the Treatment of Brain Metastases: The Relationship Between Changes in Postoperative Magnetic Resonance Imaging Characteristics and Tumor Recurrence

Publication: Acta Neurochir (Wien). 2023 May;165(5):1379-1387. PMID: 36823478

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

Publication: Data Brief. 2023 Apr 7;48:109122. PMID: 37128587 | PDF

Authors: Zwick BF, Safdar S, Bourantas GC, Joldes GR, Hyde DE, Warfield SK, Wittek A, Miller K.

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" [1] that is available for download from the Zenodo data repository (https://zenodo.org/record/7687631) [2]. 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 [3], 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

Authors: Kothurkar R, Lekurwale R, Gad M, Rathod CM.

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

Publication: Indian J Radiol Imaging. 2023 Apr 28;33(3):338-343. PMID: 37362372 | PDF

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

Publication: Brain Behav. Apr;13(4):e2929. PMID: 36879365

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.

Abstract:

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 Mar 6. 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

Publication: Osteoarthr Cartil Open. 2023 Mar 16;5(2):100356. PMID: 37008822 | PDF

Authors: Dima R, Birmingham TB, Philpott HT, Bryant D, Fenster A, Appleton CT.

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

Publication: Int J Comput Assist Radiol Surg. 2023 Mar;18(3):537-44. PMID: 36173542

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

Publication: J Imaging. 2023 Feb 20;9(2):51. PMID: 36826970

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

Publication: Sci Rep. 2023 Feb 17;13(1):2850. PMID: 36801943 | PDF

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

Publication: Cureus. 2023 Feb 7;15(2):e34756. PMID: 36777972 | PDF

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

Publication: World Neurosurg. 2023 Feb;170:e28-e36. PMID: 36270590

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.

Abstract:

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

Publication: Pediatr Radiol. 2023 Feb;53(2):282-96. PMID: 35994062

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

Publication: Eur Arch Otorhinolaryngol. 2023 Feb;280(2):919-24. PMID: 36149490

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

Publication: Eur Arch Otorhinolaryngol. 2023 Feb;280(2):671-80. PMID: 35789285

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.

Development of a Navigable 3D Virtual Model of Temporal Bone Anatomy

Publication: J Vis Commun Med. 2023 Jan 26:1-5. PMID: 36704866 | PDF

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

Publication: J Clin Med. 2023 Jan 24;12(3):920. PMID: 36769568 | PDF

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

Publication: Zhonghua Yi Xue Za Zhi. 2023 Jan 17;103(3):178-185. PMID: 36649988

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

Publication: Front Oncol. Neurosurgery. 2023 Jan 1;92(1):179-85. PMID: 36170168

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.

Abstract:

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

Publication: Zhonghua Wai Ke Za Zhi. 2023 Jan 1;61(1):61-65. PMID: 36603886 | PDF

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

Publication: Sci Rep. 2023 Jan 18;13(1):969. PMID: 36653482 | PDF

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

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

Publication: Eur J Paediatr Neurol. 2023 Jan 7;42:126-32. PMID: 36641854

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

Publication: J Coll Physicians Surg Pak. 2023 Jan;33(1):109-11. PMID: 36597246

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.

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.

Abstract: 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.

@@ Line 169: / Line 169: @@
 '''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==
+{| width="100%"
+|
+'''Publication:''' [https://pubmed.ncbi.nlm.nih.gov/37259659 J Musculoskelet Neuronal Interact. 2023 Jun 1;23(2):196-204. PMID: 37259659] | [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10233225/pdf/JMNI-23-196.pdf PDF]
+'''Authors:''' Tekin ZN, Dogruoz Karatekin B, Dogan MB, Bilgi Z.
+'''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 [http://www.slicer.org '''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==

Difference between revisions of "Main Page/SlicerCommunity/2023"

Revision as of 20:35, 10 July 2023

Contents

2023

Magnetic Resonance Imaging in Naso-Oropharyngeal Carcinoma: Role of Texture Analysis in the Assessment of Response to Radiochemotherapy, a Preliminary Study

BabelBrain: An Open-Source Application for Prospective Modeling of Transcranial Focused Ultrasound for Neuromodulation Applications

Volumetric Analysis of the Sinus and Orbit in Silent Sinus Syndrome After Endoscopic Sinus Surgery

Safety and Efficacy of Thoracic Endovascular Aortic Repair for Acute Stanford Type B Aortic Dissection With Retrograde Type a Intramural Hematoma

Multimodal Measurements of Levator Bowl Volume in Nulligravid Asymptomatic Women: Endovaginal Ultrasound Versus MRI

The Traction Force of the Pulled Limb in Hip Arthroscopic Surgery Is Determined by Stiffness Coefficient Which Is Significantly Related to Muscle Volume

Three-Dimensional Assessment of Tongue Cancer Prognosis by Preoperative MRI

Multimodal Measurements of Levator Bowl Volume in Nulligravid Asymptomatic Women: Endovaginal Ultrasound Versus MRI

Pectoralis Muscle Area Measured at T4 Level Is Closely Associated With Adverse COVID-19 Outcomes in Hospitalized Patients

Precise Location of the Ventricular Catheter Tip in Ventriculoperitoneal Shunt Placement Guided by 3D Printed Individualized Guide

PIRET-A Platform for Treatment Planning in Electroporation-Based Therapies

Surgically Assisted Maxillary Expansion With or Without Pterygoid Disjunction Alters Maxillomandibular Positioning

3D Printing Personalized Guide Plate in the Management of Recurrent Intramuscular Venous Malformations: A Single Center Experience

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

Application of Preoperative Multimodal Image Fusion Technique in Microvascular Decompression Surgery via Suboccipital Retrosigmoid Approach

Laser Interstitial Thermal Therapy in the Treatment of Brain Metastases: The Relationship Between Changes in Postoperative Magnetic Resonance Imaging Characteristics and Tumor Recurrence

Image Data and Computational Grids for Computing Brain Shift and Solving the Electrocorticography Forward Problem

ImFinite Element Analysis of a Healthy Knee Joint at Deep Squatting for the Study of Tibiofemoral and Patellofemoral Contact

A Comparison of Machine Learning Models for Survival Prediction of Patients with Glioma Using Radiomic Features from MRI Scans

Circular RNA hsa_circ_0000690 as a Potential Biomarker for Diagnosis and Prognosis of Intracranial Aneurysm: Closely Relating to the Volume of Hemorrhage

Can Quantitative Peritumoral CT Radiomics Features Predict the Prognosis of Patients With Non-Small Cell Lung Cancer? A Systematic Review

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)

Cross-Sectional Reliability and Concurrent Validity of a Quantitative 2-Dimensional Ultrasound Image Analysis of Effusion and Synovial Hypertrophy in Knee Osteoarthritis

Patient-Specific Needle Guidance Templates Drilled Intraprocedurally for Image Guided Intervention: Feasibility Study in Swine

Automatic Landmark Identification in Cone-Beam Computed Tomography

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

Design and Analysis of HSC-BPPV Diagnostic Maneuver Based on Virtual Simulation

The Simplified Tailor-Made Workflows for a 3D Slicer-Based Craniofacial Implant Design

Predicting Transient Ischemic Attack Risk in Patients With Mild Carotid Stenosis Using Machine Learning and CT Radiomics

Deep Learning Enabled Multi-Organ Segmentation of Mouse Embryos

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

Minimizing Magnetic Resonance Image Geometric Distortion at 7 Tesla for Frameless Presurgical Planning Using Skin-Adhered Fiducials

Acute Colonic Pseudo-Obstruction Secondary to Renal Calculus: A Case Report and Review of Pathophysiology

A Novel Stereotactic Aspiration Technique for Intracerebral Hemorrhage

Morphological Evaluation of the Normal and Hydrocephalic Third Ventricle on Cranial Magnetic Resonance Imaging in Children: A Retrospective Study

Henri IV of France's Larynx 3D Reconstitution

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

A Three-Dimensionally Printed Otological Model for Cholesteatoma Mastoidectomy Training

Development of a Navigable 3D Virtual Model of Temporal Bone Anatomy

Maxillary Antral Pseudocyst Drift after Osteotome Sinus Floor Elevation with Simultaneous Implant Placement: A Case Report and Literature Review

Radiomic Analysis Based on Magnetic Resonance Imaging for Predicting PD-L2 Expression in Hepatocellular Carcinoma

Correlation Between Unilateral Internal Carotid Artery Stenosis and Asymmetric Distribution of Enlarged Perivascular Spaces in Patients With Acute Cerebral Infarction

Radiomics to Predict the Mortality of Patients With Rheumatoid Arthritis-Associated Interstitial Lung Disease: A Proof-of-Concept Study

Evaluation of the Prognosis of Acute Subdural Hematoma According to the Density Differences Between Gray and White Matter

The Knosp Criteria Revisited: 3-Dimensional Volumetric Analysis as a Predictive Tool for Extent of Resection in Complex Endoscopic Pituitary Surgery

Differentiation of Lung Metastases Originated From Different Primary Tumors Using Radiomics Features Based on CT Imaging

MRI Radiomic Features of Peritumoral Edema May Predict the Recurrence Sites of Glioblastoma Multiforme

Clinical Study on Application of 3D Slicer Software Assisted Domestic Frameless Stereotactic Robot in Biopsy of Intracranial Lesions

Liver Cirrhosis and Tumor Location Can Affect the Range of Intrahepatic Microwave Ablation Zone

A Magnetic Resonance Imaging Based Radiomics Model to Predict Mitosis Cycles in Intracranial Meningioma

Advantages of a Training Course for Surgical Planning in Virtual Reality for Oral and Maxillofacial Surgery: Crossover Study

Lesion Size and Long-Term Cognitive Outcome After Pediatric Stroke: A Comparison Between Two Techniques to Assess Lesion Size

Association Between Emphysema and Other Pulmonary Computed Tomography Patterns in COVID-19 Pneumonia

A High-Resolution Pediatric Female Whole-Body Numerical Model With Comparison to a Male Model

Anatomical Morphology and Related Angles of Foramen Ovale: A Three-dimensional Computed Tomography Reconstruction

MRI Radiomic Features of Peritumoral Edema May Predict the Recurrence Sites of Glioblastoma Multiforme

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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