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

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


The following is a sample of the research performed using 3D Slicer outside of the group that develops it. in 2019

We monitor PubMed and related databases to update these lists, but if you know of other research related to the Slicer community that should be included here please email: marianna (at) bwh.harvard.edu.

Contents

2019

Clinical Relevance of the Left Brachiocephalic Vein Anatomy for Vascular Access in Dialysis Patients

Publication: Clin Anat. 2019 Dec 31. PMID: 31891199

Authors: Vertemati M, Rizzetto F, Cassin S, Zerbi P, Giordano A, Cariati M, Gallieni M.

Institution: Institute of Human Anatomy, Department of Biomedical and Clinical Sciences "Luigi Sacco", Università degli Studi di Milano, Milan, Italy.

Abstract: INTRODUCTION: Most hemodialysis patients start renal replacement therapy with a central venous catheter (CVC). The left internal jugular vein (LIJV) is the second-choice vein for CVC positioning, after the right IJV. However, to reach the right atrium, the CVC must pass through the left brachiocephalic vein (LBV), which also drains blood from the left arm through the subclavian vein. The purpose of this study is to describe how the anatomy of the central venous system and in particular that of the LBV affects vascular access in hemodialysis patients.

MATERIALS AND METHODS: Three-dimensional (3D) virtual model reconstructions of the central thoracic veins of three hemodialysis patients were obtained from contrast-enhanced computed tomography scans acquired in the venous phase. The images were exported as DICOM files and loaded on open-source software for visualizing and analyzing the medical imaging, 3D Slicer, Windows v.4.8.1.

RESULTS: As expected, the 3D reconstructions showed that the LBV has a tortuous path with three main angulations that could be associated with external compression and stenosis. These could determine the difficulties and increased risks of venous injury during CVC placement, and an increased risk of medium to long-term catheter-associated vein thrombosis and stenosis.

CONCLUSIONS: The anatomical features of the LBV indicate that the path of a CVC from the LIJV to the right atrium is tortuous and can easily be complicated by vein injury, negatively affecting the creation of future arterio-venous vascular accesses in the left arm.

Correlation Of Spontaneous and Traumatic Anterior Skull Base Csf Leak Flow Rates with Fluid Pattern on Early, Delayed, and Subtraction Volumetric Extended Echo Train T2-Weighted MRI

Publication: J Neurosurg. 2019 Dec 27:1-9. PMID: 31881543

Authors: Rutland JW, Govindaraj S, Gill CM, Shohet M, Iloreta AMC, Bederson JB, Shrivastava RK, Delman BN.

Institution: Departments of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Abstract: OBJECTIVE: CSF leakage is a potentially fatal condition that may result when a skull base dural defect permits CSF communication between the cranial vault and sinonasal cavities. Flow rate is an important property of CSF leaks that can contribute to surgical decision-making and predispose patients to complications and inferior outcomes. Noninvasive preoperative prediction of the leak rate is challenging with traditional diagnostic tools. The present study compares fluid configurations on early and late volumetric extended echo train T2-weighted MRI by using image tracings and sequence subtraction as a novel method of quantifying CSF flow rate, and it correlates radiological results with intraoperative findings and clinical outcomes.

METHODS: A total of 45 patients met inclusion criteria for this study and underwent 3-T MRI. Imaging sequences included two identical CUBE T2 (vendor trade name for volumetric extended echo train T2) acquisitions at the beginning and end of the scanning session, approximately 45 minutes apart. Twenty-five patients were confirmed to have definitive spontaneous or traumatic anterior skull base CSF leaks. Semiautomated volumetric segmentation of CSF intensity was performed on both CUBE data sets by using 3D Slicer software, and volumes were subtracted to obtain accumulated CSF volume. These imaging-derived fluid accumulations were correlated with high- or low-flow states, as well as ultimate treatment outcomes including recurrences.

RESULTS: Of the 45 patients, 25 (55.6%) had definitive evidence of CSF leakage, and 22 (88%) of these underwent surgical repair. Patients with high-flow CSF leaks had higher early (4.058 cm3 vs 0.982 cm3, p = 0.04), late (4.58 cm3 vs 1.096 cm3, p = 0.04), and accumulated (0.53 cm3 vs 0.11 cm3, p = 0.01) fluid volume measurements than patients with low-flow leaks. The 5 (22.7%) patients who exhibited postoperative CSF leak recurrence had significantly greater early (6.30 cm3 vs 1.23 cm3, p = 0.008) and late (6.87 cm3 vs 1.45 cm3, p = 0.008) volumes. Accumulated volume was not significantly greater in patients with leak recurrence (0.58 cm3 vs 0.22 cm3, p = 0.07). Early, late, and accumulated volumes were significantly correlated with postoperative hospital stay as well as duration of postoperative lumbar drain placement (p < 0.05 for all measures).

CONCLUSIONS: High-resolution CUBE T2 MRI, coupled with precise volumetric segmentation and subtraction of sinonasal hyperintensity, not only demonstrated predictive value in differentiating low- and high-flow CSF leaks, but also correlated with postoperative complications such as leak recurrence. These findings may be useful in the clinical workup and neurosurgical management of patients with skull base CSF leaks.

DCE-MRI Assessment of Response to Neoadjuvant SABR in Early Stage Breast Cancer: Comparisons of Single Versus Three Fraction Schemes and Two Different Imaging Time Delays Post-SABR

Publication: Clin Transl Radiat Oncol. 2019 Dec 25;21:25-31. PMID: 32021911 | PDF

Authors: Mouawad M, Biernaski H, Brackstone M, Lock M, Yaremko B, Shmuilovich O, Kornecki A, Ben Nachum I, Muscedere G, Lynn K, Prato FS, Thompson RT, Gaede S, Gelman N.

Institution: Medical Biophysics, Western University, London, Ontario, Canada.

Abstract: PURPOSE: To determine the effect of dose fractionation and time delay post-neoadjuvant stereotactic ablative radiotherapy (SABR) on dynamic contrast-enhanced (DCE)-MRI parameters in early stage breast cancer patients.

MATERIALS AND METHODS: DCE-MRI was acquired in 17 patients pre- and post-SABR. Five patients were imaged 6-7 days post-21 Gy/1fraction (group 1), six 16-19 days post-21 Gy/1fraction (group 2), and six 16-18 days post-30 Gy/3 fractions every other day (group 3). DCE-MRI scans were performed using half the clinical dose of contrast agent. Changes in the surrounding tissue were quantified using a signal-enhancement threshold metric that characterizes changes in signal-enhancement volume (SEV). Tumour response was quantified using Ktrans and ve (Tofts model) pre- and post-SABR. Significance was assessed using a Wilcoxin signed-rank test.

RESULTS: All group 1 and 4/6 group 2 patients' SEV increased post-SABR. All group 3 patients' SEV decreased. The mean Ktrans increased for group 1 by 76% (p = 0.043) while group 2 and 3 decreased 15% (p = 0.028) and 34% (p = 0.028), respectively. For ve, there was no significant change in Group 1 (p = 0.35). Groups 2 showed an increase of 24% (p = 0.043), and Group 3 trended toward an increase (23%, p = 0.08).

CONCLUSION: Kinetic parameters measured 2.5 weeks post-SABR in both single fraction and three fraction groups were indicative of response but only the single fraction protocol led to enhancement in the surrounding tissue. Our results also suggest that DCE-MRI one-week post-SABR may be too early for response assessment, at least for single fraction SABR, whereas 2.5 weeks appears sufficiently long to minimize confounding acute effects.

"To correct for intra-session motion, DCE images were deformably registered to the mid-time point post-contrast image using 3D Slicer v4.8.0."

Subtraction images (A) and associated signal enhancement threshold vs volume curves (B) from representative patients for each of the three groups. The slices are approximately through the center of the tumour. The pink outline represents the skin/air interface. The single fraction images show clear evidence of an increase in the signal enhancement volume local to the tumour following SABR, and this is not seen in the 30 Gy/3 fraction patient.

Prediction of Immunohistochemistry of Suspected Thyroid Nodules by Use of Machine Learning-Based Radiomics

Publication: AJR Am J Roentgenol. 2019 Dec;213(6):1348-57. PMID: 31461321

Authors: Gu J, Zhu J, Qiu Q, Wang Y, Bai T, Yin Y.

Institution: School of Medicine and Life Sciences, University of Jinan Shandong Academy of Medical Sciences, Jinan, Shandong, China.

Abstract: OBJECTIVE. The purpose of this study was to develop and validate a radiomics model for evaluating immunohistochemical characteristics in patients with suspected thyroid nodules. MATERIALS AND METHODS. A total of 103 patients (training cohort-to-validation cohort ratio, ≈ 3:1) with suspected thyroid nodules who had undergone thyroidectomy and immunohistochemical analysis were enrolled. The immunohistochemical markers were cytokeratin 19, galectin 3, thyroperoxidase, and high-molecular-weight cytokeratin. All patients underwent CT before surgery, and a 3D Slicer was used to analyze images of the surgical specimen. Test-retest and Spearman correlation coefficient (ρ) were used to select reproducible and nonredundant features. The Kruskal-Wallis test (p < 0.05) was used for feature selection, and a feature-based model was built by support vector machine methods. The performance of the radiomic models was assessed with respect to accuracy, sensitivity, specificity, corresponding AUC, and independent validation. RESULTS. Eighty-six reproducible and nonredundant features selected from the 828 features were used to build the model. The best performance of the cytokeratin 19 model yielded accuracy of 84.4% in the training cohort and 80.0% in the validation cohort. The thyroperoxidase and galectin 3 predictive models yielded accuracies of 81.4% and 82.5% in the training cohort and 84.2% and 85.0% in the validation cohort. The performance of the high-molecular-weight cytokeratin predictive model was not good (accuracy, 65.7%) and could not be validated. CONCLUSION. A radiomics model with excellent performance was developed for individualized noninvasive prediction of the presence of cytokeratin 19, galectin 3, and thyroperoxidase based on CT images. This model may be used to identify benign and malignant thyroid nodules.

A Review on Multiplatform Evaluations of Semi-automatic Open-source Based Image Segmentation for Cranio-maxillofacial Surgery

Publication: Comput Methods Programs Biomed. 2019 Dec;182:105102. PMID: 31610359

Authors: Wallner J, Schwaiger M, Hochegger K, Gsaxner C, Zemann W, Egger J.

Institution: Medical University of Graz, Department of Oral and Maxillofacial Surgery, Graz, Austria.

Abstract: BACKGROUND AND OBJECTIVES: Computer-assisted technologies, such as image-based segmentation, play an important role in the diagnosis and treatment support in cranio-maxillofacial surgery. However, although many segmentation software packages exist, their clinical in-house use is often challenging due to constrained technical, human or financial resources. Especially technological solutions or systematic evaluations of open-source based segmentation approaches are lacking. The aim of this contribution is to assess and review the segmentation quality and the potential clinical use of multiple commonly available and license-free segmentation methods on different medical platforms.

METHODS: In this contribution, the quality and accuracy of open-source segmentation methods was assessed on different platforms using patient-specific clinical CT-data and reviewed with the literature. The image-based segmentation algorithms GrowCut, Robust Statistics Segmenter, Region Growing 3D, Otsu & Picking, Canny Segmentation and Geodesic Segmenter were investigated in the mandible on the platforms 3D Slicer, MITK and MeVisLab. Comparisons were made between the segmentation algorithms and the ground truth segmentations of the same anatomy performed by two clinical experts (n = 20). Assessment parameters were the Dice Score Coefficient (DSC), the Hausdorff Distance (HD), and Pearsons correlation coefficient (r).

RESULTS: The segmentation accuracy was highest with the GrowCut (DSC 85.6%, HD 33.5 voxel) and the Canny (DSC 82.1%, HD 8.5 voxel) algorithm. Statistical differences between the assessment parameters were not significant (p < 0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the segmentation methods and the ground truth schemes. Functionally stable and time-saving segmentations were observed.

CONCLUSION: High quality image-based semi-automatic segmentation was provided by the GrowCut and the Canny segmentation method. In the cranio-maxillofacial complex, these segmentation methods provide algorithmic alternatives for image-based segmentation in the clinical practice for e.g. surgical planning or visualization of treatment results and offer advantages through their open-source availability. This is the first systematic multi-platform comparison that evaluates multiple license-free, open-source segmentation methods based on clinical data for the improvement of algorithms and a potential clinical use in patient-individualized medicine. The results presented are reproducible by others and can be used for clinical and research purposes.

Patellar Calcar: Morphometric Analysis by Knee Magnetic ResonanceImaging and Three-dimensional Reconstruction Software-assisted

Publication: Surg Radiol Anat. 2019 Dec;41(12):1483-8. PMID: 31529166

Authors: Benavente S, Villagra J.

Institution: Universidad Católica de la Santísima Concepción, Concepción, Chile.

Abstract: PURPOSE: Patellar calcar corresponds to a greater trabecular bone density area in the patella lateral facet, whose morphometry is uncertain. This study aimed to describe patellar calcar morphometry by knee MRI and develop a 3D reconstruction software-assisted.

MATERIALS AND METHODS: Consecutive adult patients, submitted to knee MRI, between 2014 and 2017, were entered in IMPAX software. Exclusion criteria are history of patellar surgical intervention, trauma, chondromalacia, bone edema or bipartite patella. All MRI images were retrospectively reviewed by three readers. MRI patellar calcar measurements are height, width, thickness and posterior distance. 3D model protocol reconstruction: 3D Slicer software was used to design a preliminary model for each patient, and then all were automatically merged into one, which was finalized using the software segmentation tools. For 3D patellar calcar location, the transpolar axis was designed.

RESULTS: 250 MRI were analyzed, patellar calcar was present in 208 (83.2%); 101 men and 107 women. Mean age was 44.3 ± 15.6 years.

MEASUREMENTS: height 13.84 ± 2.42 mm (male: 14.50 ± 2.42; female: 13.21 ± 2.26) (p < 0.0001), width 12.21 ± 2.26 mm (male 13.14 ± 2.22; female 11.33 ± 1.93) (p < 0.0001). No statistically significant difference of thickness 0.56 ± 0.22 mm (male: 0.56 ± 0.25; female: 0.56 ± 0.20) and posterior distance 2.37 ± 0.80 mm (male: 2.46 ± 0.89; female: 2.29 ± 0.69) between genders was found. 3D model results: transpolar axis went through the patellar calcar in all the cases.

CONCLUSIONS: This study shows in a 3D model reconstruction, what was previously described in the literature, determining for the first time the patellar calcar morphometry in the knee MRI and identifying it as a regular finding in this imaging test.

Decision-making Based on 3D Printed Models in Laparoscopic Liver Resections with Intraoperative Ultrasound: A Prospective Observational Study

Publication: Eur Radiol. 2019 Nov 26. PMID: 31773294

Authors: Witowski J, Budzyński A, Grochowska A, Ballard DH, Major P, Rubinkiewicz M, Złahoda-Huzior A, Popiela TJ, Wierdak M, Pędziwiatr M.

Institution: 2nd Department of General Surgery, Jagiellonian University Medical College, Krakow, Poland.

Abstract: OBJECTIVES: The aim of this study was to evaluate impact of 3D printed models on decision-making in context of laparoscopic liver resections (LLR) performed with intraoperative ultrasound (IOUS) guidance.

METHODS: Nineteen patients with liver malignances (74% were colorectal cancer metastases) were prospectively qualified for LLR or radiofrequency ablation in a single center from April 2017 to December 2018. Models were 3DP in all cases based on CT and facilitated optical visualization of tumors' relationships with portal and hepatic veins. Planned surgical extent and its changes were tracked after CT analysis and 3D model inspection, as well as intraoperatively using IOUS.

RESULTS: Nineteen patients were included in the analysis. Information from either 3DP or IOUS led to changes in the planned surgical approach in 13/19 (68%) patients. In 5/19 (26%) patients, the 3DP model altered the plan of the surgery preoperatively. In 4/19 (21%) patients, 3DP independently changed the approach. In one patient, IOUS modified the plan post-3DP. In 8/19 (42%) patients, 3DP model did not change the approach, whereas IOUS did. In total, IOUS altered surgical plans in 9 (47%) cases. Most of those changes (6/9; 67%) were caused by detection of additional lesions not visible on CT and 3DP.

CONCLUSIONS: 3DP can be helpful in planning complex and major LLRs and led to changes in surgical approach in 26.3% (5/19 patients) in our series. 3DP may serve as a useful adjunct to IOUS.

KEY POINTS: • 3D printing can help in decision-making before major and complex resections in patients with liver cancer. • In 5/19 patients, 3D printed model altered surgical plan preoperatively. • Most surgical plan changes based on intraoperative ultrasonography were caused by detection of additional lesions not visible on CT and 3D model.

Segmentation was performed in 3D Slicer.

In-House Surgeon-Led Virtual Surgical Planning for Maxillofacial Reconstruction

Publication: J Oral Maxillofac Surg. 2019 Nov 21. PMID: 31843280

Authors: Abo Sharkh H, Makhoul N.

Institution: Maxillofacial Oncology and Microvascular Reconstruction, Department of Oral and Maxillofacial Surgery, McGill University Health Centre, Montreal, QC, Canada.

Abstract: PURPOSE: Virtual surgical planning (VSP) and custom fabricated cutting guides for maxillofacial reconstruction have been shown to improve the accuracy of bony reconstruction and overall surgical efficiency and decrease the ischemia time. Our aim was to describe an in-house VSP technique for maxillofacial reconstructive procedures.

MATERIALS AND METHODS: We used 2 free software applications. 3D Slicer was used to extract the bones of interest for the recipient and the donor sites from the computed tomography scan's DICOM (digital imaging and communications in medicine) data. The Autodesk Meshmixer (Autodesk Inc, San Rafael, CA) was used to perform VSP and fabrication of the cutting guides. A reconstructed jaw model was printed in-house using a commercially available fused deposition modeling-based desktop 3-dimensional (3D) printer (Qidi Technology, Zhejiang, China) and used to prebend the reconstruction plate. The cutting guides were printed using a commercially available resin-based stereolithography apparatus desktop 3D printer (Form 2, Dental SG Resin; Formlabs, Somerville, MA) to allow for sterilization of the guides. We performed this technique for 19 consecutive patients with maxillofacial benign or malignant tumors requiring microvascular bony reconstruction. We calculated the average time and associated costs using this in-house VSP technique.

RESULTS: The technique was found to be simple and repeatable. The average time required for VSP was 158 minutes (2 hours, 38 minutes). The average cost for printing the reconstructed model per case was $5.21 Canadian dollars (CAD), and the average cost for printing the cutting guides per case was $12.80 CAD.

CONCLUSIONS: Using this technique, in-house VSP and 3D printing can be performed by the treating surgeon, without an engineering background, within a reasonable period.

Patient-specific Access Planning in Minimally Invasive Mitral Valve Surgery

Publication: Med Hypotheses. 2019 Nov 14;136:109475. PMID: 31812012

Authors: Di Perna D, Castro M, Gasc Y, Haigron P, Verhoye JP, Anselmi A.

Institution: University of Rennes, France.

Abstract: BACKGROUND: Minimally invasive mitral valve repair or replacement (MIMVR) approaches have been increasingly adopted for the treatment of mitral regurgitation, allowing a shorter recovery time and improving postoperative quality of life. However, inadequate positioning of the right mini thoracotomy access (working port) translates into suboptimal exposure, prolonged operative times and, potentially, reduction in the quality of mitral repair. At present, we are missing tools to further improve the positioning of the working port in order to ameliorate surgical exposure in a patient- specific fashion.

METHODS AND EVALUATION OF THE HYPOTHESIS: We hypothesized that computation of relevant anatomical measurements from preoperative CT scans in patients undergoing MIMVR may provide patient-specific information in order to propose the surgical access that best fits to the patient's morphology. We hypothesized that this may systematize optimal mitral valve exposure, facilitating the procedure and potentially ameliorating the outcomes. We also hypothesized that preoperative simulation of the working port site and surgical instruments' insertion using a three-dimensional virtual model of the patient is feasible and may help in the customization of ports positioning. The hypothesis was evaluated by a multidisciplinary team including cardiac surgeons, experts in medical image processing and biomedical engineers. CT scans of 14 patients undergoing MIMVR were segmented to visualize 3D chest bones and heart structures meshes. The mitral valve annulus is pointed manually by the expert or extracted automatically when contrast-enhanced CT scan was available. The valve plane was then calculated and the optimal incision location analyzed according to a) the perpendicularity and b) the distance between the intercostal spaces and the valve plane. An angle-chart representation for the 4th, 5th and 6th intercostal spaces and a color map illustrating the distance between the skin and the mitral valve were created. We started the development of a simulation tool for preoperative planning using 3D Slicer software.

CONCLUSIONS: Several patient-specific factors (including the orientation of the mitral valve plane and the morphology of the chest cage) may influence the performance of a MIMVR procedure, but they are not quantitatively considered in the current planning strategy. We suggest that the clinical results of MIMVR can be improved through preoperative virtual simulation and computer-assisted surgery (through determination of working port and surgical instruments insertion positioning). Further research is justified and the development of a software tool for clinical evaluation is warranted to verify the current hypothesis.

Spatial Accuracy of a Clinically Established Noninvasive Electrocardiographic Imaging System for the Detection of Focal Activation in an Intact Porcine Model

Publication: Circ Arrhythm Electrophysiol. 2019 Nov;12(11):e007570. PMID: 31707808 | PDF

Authors: Hohmann S, Rettmann ME, Konishi H, Borenstein A, Wang S, Suzuki A, Michalak GJ, Monahan KH, Parker KD, Newman LK, Packer DL.

Institution: Translational Interventional Electrophysiology Laboratory, Mayo Clinic, Rochester, MN, USA.

Abstract: BACKGROUND: Noninvasive electrocardiographic imaging (ECGi) is used clinically to map arrhythmias before ablation. Despite its clinical use, validation data regarding the accuracy of the system for the identification of arrhythmia foci is limited.

METHODS: Nine pigs underwent closed-chest placement of endocardial fiducial markers, computed tomography, and pacing in all cardiac chambers with ECGi acquisition. Pacing location was reconstructed from biplane fluoroscopy and registered to the computed tomography using the fiducials. A blinded investigator predicted the pacing location from the ECGi data, and the distance to the true pacing catheter tip location was calculated.

RESULTS: A total of 109 endocardial and 9 epicardial locations were paced in 9 pigs. ECGi predicted the correct chamber of origin in 85% of atrial and 92% of ventricular sites. Lateral locations were predicted in the correct chamber more often than septal locations (97% versus 79%, P=0.01). Absolute distances in space between the true and predicted pacing locations were 20.7 (13.8-25.6) mm (median and [first-third] quartile). Distances were not significantly different across cardiac chambers.

CONCLUSIONS: The ECGi system is able to correctly identify the chamber of origin for focal activation in the vast majority of cases. Determination of the true site of origin is possible with sufficient accuracy with consideration of these error estimates.

"3D Slicer v.4.10.0 was used to integrate the CT imaging and 3D model data, and for visualization purposes."

Study and analysis workflow. A, Animal with ECG acquisition vest. B, Geometric reconstruction of fiducial marker and catheter tip positions in 3D from corresponding biplane fluoroscopy images. Top, Measurements of clip and catheter positions in a set of biplane fluoroscopy images. This is shown for one clip and the catheter tip only but was performed for all clips and the catheter tip. Bottom, Reconstruction of a 3D point cloud from biplane fluoroscopy images. Each point (red sphere) is located at the intersection of its two projection vectors shown as red dashed lines. C, Electrocardiographic imaging (ECGi) map. ECGi information represented as isopotential lines on the segmented ventricular surface, from −2.8 mV (white) to +3.66 mV (dark green). The location of the earliest negativity has been marked by the purple marker. D, Corresponding volume rendered computed tomography (CT), oriented in the same caudal right posterior oblique view as (C). The inferior aspect of the heart is shown. The purple marker corresponds to the purple marker in (C). The green marker identifies the true pacing location as reconstructed from fluoroscopy (near the RV apex). Euclidean distance between the 2 points in space was 17.9 mm in this case.
]

Direct Evidence for Eudicot Pollen-feeding in a Cretaceous Stinging Wasp (Angiospermae; Hymenoptera, Aculeata) Preserved in Burmese Amber

Publication: Commun Biol. 2019 Nov 7;2:408. PMID: 31728419 | PDF

Authors: Grimaldi DA, Peñalver E, Barrón E, Herhold HW, Engel MS.

Institution: American Museum of Natural History, New York, NY, USA.

Abstract: Angiosperms and their insect pollinators form a foundational symbiosis, evidence for which from the Cretaceous is mostly indirect, based on fossils of insect taxa that today are anthophilous, and of fossil insects and flowers that have apparent anthophilous and ento- mophilous specializations, respectively. We present exceptional direct evidence preserved in mid-Cretaceous Burmese amber, 100 mya, for feeding on pollen in the eudicot genus Tri- colporoidites by a basal new aculeate wasp, Prosphex anthophilos, gen. et sp. nov., in the lineage that contains the ants, bees, and other stinging wasps. Plume of hundreds of pollen grains wafts from its mouth and an apparent pollen mass was detected by micro-CT in the buccal cavity: clear evidence that the wasp was foraging on the pollen. Eudicots today comprise nearly three-quarters of all angiosperm species. Prosphex feeding on Tricolporoidites supports the hypothesis that relatively small, generalized insect anthophiles were important pollinators of early angiosperms.

Post-processing and analysis performed in 3D Slicer.

CT images and illustrations of the holotype of P. anthophilos, new genus, new species, AMNH Bu-KL18-31. a CT image, external surface. Portions of thin and/or distorted cuticle are missing, particularly in the mid-section. b, c Two CT slices through (a), showing the longitudinal (b) and dorsoventral flight muscles (c), walls of the crop (b), and a high-density mass in the buccal cavity (c), likely a pollen mass that is partially pyritized. d–h Illustrated rendering of Prosphex, showing the forewing (d, with conventional abbreviations for wing veins and cells) and the hind wing (e) (slightly reconstructed), dorsal view of head and thorax (f), left ventrolateral habitus (g: cx, coxa) and detail of sting (h). Body of the wasp is rendered as preserved, without reconstruction. All images to the same scale (scale line 1.0 mm); h is slightly magnified
]

Whole Lesion Histogram Analysis of Apparent Diffusion Coefficients on MRI Predicts Disease-free Survival in Locally Advanced Squamous Cell Cervical Cancer after Radical Chemo-radiotherapy

Publication: BMC Cancer. 2019 Nov 15;19(1):1115. PMID: 31729974 | PDF

Authors: Zhao B, Cao K, Li XT, Zhu HT, Sun YS.

Institution: Department of Radiology, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital and Institute, Beijing, China.

Abstract: BACKGROUND: The aim was to investigate the prognostic value of MR apparent diffusion coefficients (ADC) using histogram analysis (HA) in predicting disease-free survival (DFS) of cervical cancer after chemo-radiation therapy.

METHODS: We retrospectively analyzed 103 women with pathologically proven squamous cell uterine cancer who received chemo-radiation therapy between 2009 and 2013. All patients were followed up for more than 2 years. Pre-treatment MR images were retrieved and imported for HA using an in-house developed software program based on 3D Slicer. Regions of interest of whole tumors were drawn manually on DWI with reference to T2WI. HA features (mean, max, min, 50, 10, 90%, kurtosis, and skewness) were extracted from apparent diffusion coefficient (ADC) maps and compared between the recurrence and non-recurrence groups after the 2-year follow-up. Univariate and multivariate Cox regression analysis was used to correlate ADC HA features and relevant clinical variables (age, grade, maximal diameter of tumor, FIGO stage, SCC-Ag) with DFS.

RESULTS: One hundred three patients with stage IB-IV cervical cancers were followed up for 2.0-94.6 months (median 48.9 months). Twenty patients developed recurrence within 2 years. In the recurrence group, the min (P = 0.001) and 10% (P = 0.048) ADC values were significantly lower than those of the non-recurrence group. Univariate and multivariate Cox regression analysis revealed that ADCmin (P = 0.006, HR = 0.110) was significantly correlated with DFS.

CONCLUSION: Pre-treatment volumetric ADCmin in histogram analysis is an independent factor that is correlated with DFS in cervical cancer patients treated with chemo-radiation therapy.

Manual segmentation of ROIs in cervical lesion and schematic diagram of parameters. a–c Referring to T2WI and DWI, ROIs were drawn manually slice by slice on DWI images along the edge of the lesions in order to cover as much tumor area as possible without excluding cystic or necrotic areas. d The same ROIs were registered to ADC maps.
]

Variations in the Size and Shape of Human Cochlear Malformation Types

Publication: Anat Rec (Hoboken). 2019 Oct;302(10):1792-9. PMID: 30980504 | PDF

Authors: Dhanasingh A.

Institution: MED-EL GmbH, Innsbruck, Austria.

Abstract: The objective of this study is to determine the variations in size and shape of the most widely recognized cochlear malformation types using three-dimensional (3D) visualization. Using 3D Slicer freeware, the complete inner-ear structures were segmented from 46 anonymized high-resolution computed tomography (HRCT) image datasets. Cochlear height, internal auditory canal height, and width were measured from the axial plane. Cochlear basal turn diameter was measured from the oblique coronal plane. Number of cochlear turns was measured from the 3D images and the corresponding cochlear duct length (CDL) was estimated using the CDL equations given in Alexiades et al. [Otol Neurotol 36 (2015) 904-907]. Out of 46 preoperative HRCT image datasets of human temporal bone, cochlear anatomy types including normal anatomy (4), enlarged vestibular aqueduct syndrome (3), cochlear aplasia (2), incomplete partition Types I (8), II (Mondini's deformity) (3), and III (X-linked) (4), cochlear hypoplasia (CH) (17), and common cavity (CC) (5) were identified. Majority of CH cases had cochlear height shorter than 4 mm whereas the CC cases measured cochlear height above 6 mm. For all the other malformation types, cochlear height was between 4 and 6 mm. In terms of "A" value, majority of CH cases showed shorter "A" value of <7.5 mm, which is in the lower end in comparison to the rest of the malformation types reported in this study. 3D-visualization shows the size and shape variations of all the structures of inner ear and also improves the clinicians' ability to visualize cochlear anatomy and nearby structures much easier than from the 2D image slices.

Volumetric Assessment of the Dental Crown for Sex Estimation by Means of Cone-beam Computed Tomography

Publication: Forensic Sci Int. 2019 Oct;303:109920. PMID: 31442711

Authors: Manhaes-Caldas D, Oliveira ML, Groppo FC, Haiter-Neto F.

Institution: Department of Oral Diagnosis, Division of Oral Radiology, Piracicaba Dental School, University of Campinas, São Paulo, Brazil.

Abstract: Sex estimation has a vital role in the solution of forensic cases when the identification of a large number of victims is needed. Considering the sexual dimorphism of the human teeth, the objective of this study was to estimate human sex by means of cone beam computed tomography (CBCT)-based volumetric assessment of the dental crown. A total of 78 CBCT images of the upper central incisors, upper and lower canines, and lower lateral incisors were equally selected from a Brazilian population aged between 8 and 36 years old. The dental crowns were subjected to image-based volumetric assessment by manual segmentation using the 3D Slicer software, and the outcomes were compared by the Mann-Whitney test, unpaired t-test, Pearson correlation test, conditional backward stepwise logistic regression and intraclass correlation coefficient (α=0.05). The volumetric accuracy of the upper central incisor, upper canine and lower canine for sex estimation were 64.1%, 74.4% and 79.5%, respectively. The combined analysis of the upper and lower canines allowed an average accuracy of 83.7%. In conclusion, the combined volumetric analysis of the crown of the upper and lower canines can be applied for sex estimation in the studied population.

Association of Serum Cystatin C with White Matter Abnormalities in Patients with Amnestic Mild Cognitive Impairment

Publication: Geriatr Gerontol Int. 2019 Oct;19(10):1036-40. PMID: 31489777 | PDF

Authors: Hirao K, Yamashita F, Tsugawa A, Haime R, Fukasawa R, Sato T, Okita M, Shimizu S, Kanetaka H, Umahara T, Sakurai H, Hanyu H.

Institution: Department of Geriatric Medicine, Tokyo Medical University, Tokyo, Japan.

Abstract: AIM: White matter hyperintensities (WMH) on MRI have been reported to be a risk factor for the conversion from mild cognitive impairment (MCI) to Alzheimer's disease, although the reason remains unclear. In the present study, we hence investigated the associations between WMH volumes and cognitive function, blood levels of various molecules, and the presence of lifestyle-associated diseases in patients with amnestic MCI.

METHODS: The initial data of 38 patients with amnestic MCI and 10 normal control individuals were analyzed. The volumes of periventricular hyperintensities (PVH) and deep WMH (DWMH) were measured on T2 fluid-attenuated inversion recovery using the imaging software, 3D Slicer; and the association between PVH/DWMH volumes and cognitive function, blood levels of molecules (such as cystatin C [CysC], 25-hydroxyvitamin D and homocysteine) and the presence of lifestyle-associated diseases (such as hypertension, hyperlipidemia and diabetes mellitus) were analyzed.

RESULTS: In the MCI group, the PVH volume : intracranial volume ratio significantly correlated with Trail Making Test-A/B scores and CysC level by Pearson's analysis, and the PVH volume : intracranial volume ratio significantly correlated with only CysC levels, whereas the DWMH volume : intracranial volume ratio did not correlate with any items at all by linear multiple regression analysis.

CONCLUSIONS: PVH volume was closely associated with frontal lobe dysfunction, particularly with attention and executive dysfunction. Serum CysC level was associated with PVH volume, which suggests that CysC might be a useful marker for determining treatment strategies for white matter abnormalities in amnestic MCI.

Three-dimensional Clavicle Displacement Analysis and its Effect on ScapularPosition in Acute Clavicle Midshaft Fracture

Publication: J Shoulder Elbow Surg. 2019 Oct;28(10):1877-85. PMID: 31272891

Authors: Kim JH, Gwak HC, Kim CW, Lee CR, Kim YJ, Seo HW.

Institution: Department of Orthopedic Surgery, Inje University Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea.

Abstract:BACKGROUND: The purpose of this study was to measure the distance of the clavicle in 3 dimensions (3D) and each direction (anterior to posterior, medial to lateral, and superior to inferior) and to analyze the correlation of the angular orientation of the scapula according to each directional distance of the clavicle.

METHODS: Sixty-seven patients with Robinson 2B1 and 2B2 clavicle midshaft fracture (46.0 ± 17.4 years, men = 50, women = 17) were selected as final subjects. Patients' computed tomography was reconstructed using an image processing program (3D Slicer v.4.3 software). Anteroposterior (AP) distance, medial-to-lateral distance, superior-to-inferior distance, and 3D distance of both clavicles were measured. The plane connecting the 3 points (superior pole, inferior pole, and center of glenoid) of the scapula was used to calculate differences in the angular orientation between both scapulae.

RESULTS: Among each directional distance of the clavicle, only the AP distance showed negative correlation with scapular angular orientation with anterior tilting, internal rotation, and upward rotation of the scapula (Pearson's correlation coefficient: -0.68, -0.24, and -0.28; P < .001, P = .048, and P = .021).

CONCLUSION: The shortening of the AP distance of the clavicle was related to the angular orientation of the scapula in acute clavicle fracture. AP shortening should be considered when determining the treatment of clavicle fracture.

Mammographic Breast Density Assessed with Fully Automated Method and its Risk for Breast Cancer

Publication: J Clin Imaging Sci. 2019 Oct 11;9:43. PMID: 31662951 | PDF

Authors: Saikiran P, Ramzan R, Nadish S, Kamineni PD, Priyanka, John AM.

Institution: Department of Medical Imaging Technology, Manipal College of Health Professions, Manipal, Karnataka, India.

Abstract:

OBJECTIVES: We evaluated the association between breast cancer and breast density (BD) measured using fully automated software. We also evaluated the performance of cancer risk models such as only clinical risk factors, density related measures, and both clinical risk factors and density-related measures for determining cancer risk.

MATERIALS AND METHODS: This is a retrospective case-control study. The data were collected from August 2015 to December 2018. Two hundred fifty women with breast cancer and 400 control subjects were included in this study. We evaluated the BD qualitatively using breast imaging-reporting and data system density and quantitatively using 3D Slicer. We also collected clinical factors such as age, familial history of breast cancer, menopausal status, number of births, body mass index, and hormonal replacement therapy use. We calculated the odds ratio (OR) for BD to determine the risk of breast cancer. We performed receiver operating characteristic (ROC) curve to assess the performance of cancer risk models.

RESULTS: The OR for the percentage BD for second, third, and fourth quartiles was 1.632 (95% confidence intervals [CI]: 1.102-2.416), 2.756 (95% CI: 1.704-4.458), and 3.163 (95% CI: 1.356-5.61). The area under ROC curve for clinical risk factors only, mammographic density measures, combined mammographic, and clinical risk factors was 0.578 (95% CI: 0.45, 0.64), 0.684 (95% CI: 0.58, 0.75), and 0.724 (95% CI: 0.64, 0.80), respectively.

CONCLUSION: Mammographic BD was found to be positively associated with breast cancer. The density related measures combined clinical risk factors, and density model had good discriminatory power in identifying the cancer risk.

(a) Left craniocaudal mammogram of a 41-year-old woman with a negative screening exam (b) example of density segmentation using 3D slicer software tool showing automatic identification of mammographic density.

A review on Multiplatform Evaluations of Semi-automatic Open-source Based Image Segmentation for Cranio-maxillofacial Surgery

Publication: Comput Methods Programs Biomed. 2019 Sep 30;182:105102. PMID: 31610359

Authors: Wallner J, Schwaiger M, Hochegger K, Gsaxner C, Zemann W, Egger J.

Institution: Medical University of Graz, Department of Oral and Maxillofacial Surgery, Graz, Austria.

Abstract: BACKGROUND AND OBJECTIVES: Computer-assisted technologies, such as image-based segmentation, play an important role in the diagnosis and treatment support in cranio-maxillofacial surgery. However, although many segmentation software packages exist, their clinical in-house use is often challenging due to constrained technical, human or financial resources. Especially technological solutions or systematic evaluations of open-source based segmentation approaches are lacking. The aim of this contribution is to assess and review the segmentation quality and the potential clinical use of multiple commonly available and license-free segmentation methods on different medical platforms.

METHODS: In this contribution, the quality and accuracy of open-source segmentation methods was assessed on different platforms using patient-specific clinical CT-data and reviewed with the literature. The image-based segmentation algorithms GrowCut, Robust Statistics Segmenter, Region Growing 3D, Otsu & Picking, Canny Segmentation and Geodesic Segmenter were investigated in the mandible on the platforms 3D Slicer, MITK and MeVisLab. Comparisons were made between the segmentation algorithms and the ground truth segmentations of the same anatomy performed by two clinical experts (n = 20). Assessment parameters were the Dice Score Coefficient (DSC), the Hausdorff Distance (HD), and Pearsons correlation coefficient (r).

RESULTS: The segmentation accuracy was highest with the GrowCut (DSC 85.6%, HD 33.5 voxel) and the Canny (DSC 82.1%, HD 8.5 voxel) algorithm. Statistical differences between the assessment parameters were not significant (p < 0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the segmentation methods and the ground truth schemes. Functionally stable and time-saving segmentations were observed.

CONCLUSION: High quality image-based semi-automatic segmentation was provided by the GrowCut and the Canny segmentation method. In the cranio-maxillofacial complex, these segmentation methods provide algorithmic alternatives for image-based segmentation in the clinical practice for e.g. surgical planning or visualization of treatment results and offer advantages through their open-source availability. This is the first systematic multi-platform comparison that evaluates multiple license-free, open-source segmentation methods based on clinical data for the improvement of algorithms and a potential clinical use in patient-individualized medicine. The results presented are reproducible by others and can be used for clinical and research purposes.


Potential Role of Convolutional Neural Network Based Algorithm in Patient Selection for DCIS Observation Trials Using a Mammogram Dataset

Publication: Acad Radiol. 2019 Sep 13. PMID: 31526687

Authors: Mutasa S, Chang P, Van Sant EP, Nemer J, Liu M, Karcich J, Patel G, Jambawalikar S, Ha R.

Institution: Department of Medical Physics and Radiology, Columbia University Medical Center, NY, USA.

Abstract: RATIONALE AND OBJECTIVES: We investigated the feasibility of utilizing convolutional neural network (CNN) for predicting patients with pure Ductal Carcinoma In Situ (DCIS) versus DCIS with invasion using mammographic images.

MATERIALS AND METHODS: An IRB-approved retrospective study was performed. 246 unique images from 123 patients were used for our CNN algorithm. In total, 164 images in 82 patients diagnosed with DCIS by stereotactic-guided biopsy of calcifications without any upgrade at the time of surgical excision (pure DCIS group). A total of 82 images in 41 patients with mammographic calcifications yielding occult invasive carcinoma as the final upgraded diagnosis on surgery (occult invasive group). Two standard mammographic magnification views (CC and ML/LM) of the calcifications were used for analysis. Calcifications were segmented using an open source software platform 3D Slicer and resized to fit a 128 × 128 pixel bounding box. A 15 hidden layer topology was used to implement the neural network. The network architecture contained five residual layers and dropout of 0.25 after each convolution. Five-fold cross validation was performed using training set (80%) and validation set (20%). Code was implemented in open source software Keras with TensorFlow on a Linux workstation with NVIDIA GTX 1070 Pascal GPU.

RESULTS: Our CNN algorithm for predicting patients with pure DCIS achieved an overall diagnostic accuracy of 74.6% (95% CI, ±5) with area under the ROC curve of 0.71 (95% CI, ±0.04), specificity of 91.6% (95% CI, ±5%) and sensitivity of 49.4% (95% CI, ±6%).

CONCLUSION: It's feasible to apply CNN to distinguish pure DCIS from DCIS with invasion with high specificity using mammographic images.

Texture Analysis of Pretreatment 18FFDG PET/CT for the Prognostic Prediction of Locally Advanced Salivary Gland Carcinoma Treated with Interstitial Brachytherapy

Publication: EJNMMI Res. 2019 Sep 11;9(1):89. PMID: 31511990 | PDF

Authors: Wu WJ, Li ZY, Dong S, Liu SM, Zheng L, Huang MW, Zhang JG.

Institution: Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Somatology, Beijing, China.

Abstract: BACKGROUND: The aim of this study was to evaluate the prognostic value of positron emission tomography (PET) parameters and the PET texture features of fluorine 18-fluorodeoxyglucose ([18F]FDG) uptake on pretreatment PET/computed tomography (CT) in patients with locally advanced salivary gland carcinoma treated with interstitial brachytherapy.

METHODS: Forty-three patients with locally advanced salivary gland carcinoma of the head and neck were treated with 125I interstitial brachytherapy as the sole modality and underwent 18FFDG PET/CT scanning before treatment. Tumor segmentation and texture analysis were performed using the 3D Slicer software. In total, 54 features were extracted and categorized as first-order statistics, morphology and shape, gray-level co-occurrence matrix, and gray-level run length matrix. Up to November 2018, the follow-up time ranged from 6 to 120 months (median 18 months). Cumulative survival was calculated by the Kaplan-Meier method. Factors between groups were compared by the log-rank test. Multivariate Cox regression analysis with a backward conditional method was used to predict progression-free survival (PFS).

RESULTS: The 3- and 5-year locoregional control (LC) rates were 55.4% and 37.0%, respectively. The 3- and 5-year PFS rates were 51.2% and 34.1%, respectively. The 3- and 5-year overall survival (OS) rates were 77.0% and 77.0%, respectively. Univariate analysis revealed that minimum intensity, mean intensity, median intensity, root mean square, and long run emphasis (LRE) were significant predictors of PFS, whereas clinicopathological factors, conventional PET parameters, and PET texture features failed to show significance. Multivariate Cox regression analysis showed that minimum intensity and LRE were significant predictors of PFS.

CONCLUSIONS: The texture analysis of pretreatment [18F]FDG PET/CT provided more information than conventional PET parameters for predicting patient prognosis of locally advanced salivary gland carcinoma treated with interstitial brachytherapy. The minimum intensity was a risk factor for PFS, and LRE was a favorable factor in prognostic prediction according to the primary results.

The procedure of brachytherapy based on PET/CT figure: Pretreatment PET/CT showed a T4 parotid gland carcinoma (a). Quality verification using postoperative CT images in the brachytherapy treatment planning system showed that the D90 curve covered the tumor area (b). PET/CT showed that the area of focal FDG uptake regressed 6 months after brachytherapy (c). Dose-volume histograms of the target area and organs at risk are shown (d). ICA internal carotid artery, SC spinal cord, EAC external auditory canal.
]

Levator Bowl Volume during Straining and its Relationship to other Levator Measures

Publication: Int Urogynecol J. 2019 Sep;30(9):1457-63. PMID: 31222569

Authors: Nandikanti L, Sammarco AG, Chen L, Ashton-Miller JA, DeLancey JO.

Institution: School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Abstract: INTRODUCTION AND HYPOTHESIS: This study was aimed at measuring levator ani bowl volume at rest and while straining, comparing women with and without prolapse (controls), and assessing the ability of measures of the mid-sagittal bowl area, levator hiatus (LH), and urogenital hiatus (UGH) to predict bowl volume.

METHODS: Forty MRI scans previously acquired in case-control prolapse studies, including 20 women with prolapse and 20 women without prolapse, of similar age and parity, were selected. 3D models of rest and strain bowl volumes were made using sagittal scans and 3D Slicer. Mid-sagittal bowl area, UGH, and LH were measured using ImageJ. Data were analyzed using two sample t tests, effect sizes, and Pearson's correlation coefficients at the 0.05 significance level.

RESULTS: Data were acquired in a total of 40 total women. Levator bowl volume at strain had a correlation coefficient of 0.5 with bowl volume at rest. During straining, prolapse subjects had a 53% larger bowl volume than control subjects (254 ± 86 cm3 vs 166 ± 44 cm3, p < 0.001), but at rest, the difference was 34% (138 ± 40 cm3 vs 103 ± 25 cm3, p = 0.002). Effect sizes for all parameters were large (d > 0.75). The strongest correlation with straining bowl volume was mid-sagittal straining bowl area (r = 0.86), followed by LH strain (r = 0.80), then UGH strain (r = 0.76).

CONCLUSIONS: Straining levator bowl volume is substantially different than measures made at rest, with only a quarter of straining values explained by resting measurements. The bowl area at strain is the best 2D measurement estimating bowl volume and explains 74% of straining bowl volume.


Funding:

  • P50 HD044406/HD/NICHD NIH HHS/United States
  • R01 HD038665/HD/NICHD NIH HHS/United States

Mixed Reality-Based Preoperative Planning for Training of Percutaneous Transforaminal Endoscopic Discectomy: A Feasibility Study.

Publication: World Neurosurg. 2019 Sep;129:e767-e775. PMID: 31203062

Authors: Yu H, Zhou Z, Lei X, Liu H, Fan G, He S.

Institution: Orthopedic Department, Shanghai Tenth People's Hospital, Shanghai, China.

Abstract: OBJECTIVE: To explore the effect of preoperative planning using mixed reality (MR) on training of percutaneous transforaminal endoscopic discectomy (PTED).

METHODS: Before the training, we invited an experienced chief physician to plan the puncture path of PTED on the X-ray films of the lumbar spine model and the 3D Slicer platform, respectively, and used this as the standard to guide trainees. In the aggregate, 60 young residents were randomly divided into Group A (N = 30) and Group B (N = 30). Group A learned the 2-dimensional standard planning route, whereas Group B learned the standard route planning based on MR through the 3D Slicer platform. Then, trainees were asked to conduct PTED puncture on a lumbar spine model. Questionnaires were distributed to trainees before and after the training. During the training, puncture times, operating time (minutes), and fluoroscopy times were recorded.

RESULTS: After the training, it was obvious that more trainees showed their recognition of MR, believing that MR could help preoperative planning and training of PTED. Their high satisfaction with the training indicated the success of our training. Moreover, puncture times, operating time (minutes), and fluoroscopy times of Group B were significantly lower than those of Group A.

CONCLUSIONS: MR technology contributes to preoperative planning of PTED and is beneficial in the training of PTED. It significantly reduces puncture times and fluoroscopy times, providing a standardized method for the training of PTED.

Evaluation of Accuracy of a Three-Dimensional Printed Model in Open-Wedge High Tibial Osteotomy

Publication: J Knee Surg. 2019 Sep;32(9):841-6. PMID: 30189435 | PDF

Authors: Kim HJ, Park J, Park KH, Park IH, Jang JA, Shin JY, Kyung HS.

Institution: Department of Orthopaedic Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea.

Abstract: The purpose of this study was to evaluate the usefulness of a three-dimensional (3D) printed model for open-wedge high tibial osteotomy (HTO). This study retrospectively evaluated 20 patients with medial knee osteoarthritis and varus deformity. Between October 2015 and July 2016, the patients underwent open-wedge HTO using a 3D printed model. The mean age of patients was 55.2 years (range, 51-60 years). The mean preoperative mechanical femorotibial angle (mFTA) was varus 7.8 degrees (range, varus 4.7-11.6 degrees). After measuring the target angle using full-length lower limb weight-bearing radiography, the osteotomy was simulated using 3D images obtained from computed tomography (CT) with the 3D Slicer program. On the basis of the simulated osteotomy section and the target angle, the model was then designed and printed. Open-wedge HTO was then performed by applying the 3D printed model to the opening gap. The accuracy of osteotomy and the change in posterior tibial slope (PTS) angle were evaluated. The weight-bearing line on the tibial plateau was corrected from a preoperative mean of 19.5 ± 9.8% to a postoperative mean of 63.1 ± 6.1% (p < 0.001). The postoperative values were not statistically significantly different from the preoperative target points (p = 0.688). The mFTA was corrected to a postoperative mean of valgus 3.8 ± 1.4 degrees. The PTS angle showed no significant change (p = 0.256). A 3D printed model using CT may be useful for preoperative planning of open-wedge HTO. Satisfactory correction can be obtained without a change in the PTS.


Technique Development and Measurement of Cross-Sectional Area of the Pubovisceral Muscle on MRI Scans of Living Women

Publication: Int Urogynecol J. 2019 Aug;30(8):1305-12. PMID: 29974138

Authors: Masteling M, Ashton-Miller JA, DeLancey JOL.

Institution: Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.

Abstract: INTRODUCTION AND HYPOTHESIS: Measurements of the anatomic cross-sectional area (CSA) of the pubovisceral muscle (PVM) in women are confounded by the difficulty of separating the muscle from the adjacent puborectal (PRM) and iliococcygeal (ICM) muscles when visualized in a plane orthogonal to the fiber direction. We tested the hypothesis that it might be possible to measure the PVM CSA within a defined region of interest based on magnetic resonance images (MRI).

METHODS: MRI scans of 11 women with unilateral PVM tears and seven primiparous women with intact muscles following elective C-section were used to identify the PVM injury zone defined by the mean location of its boundaries with the adjacent intact PRM and ICM from existing anatomic reference points using 3D Slicer and ImageJ software. Then, from the 15 or more 2-mm transverse slices available, the slice with the maximum anatomic CSA of the left and right PVM was found in 24 primiparous women with bilaterally intact muscles who had delivered via C-section.

RESULTS: Mean [± standard deviation (SD)] of the maximum left or right PVM cross-section areas for the 24 women, measured by two different raters, was 1.25 ± 0.29 cm2 (range 0.75-1.86). The 5th, 50th, and 95th percentile values were 0.77, 1.23, and 1.80 cm2, respectively. Inter- and intrarater measurement repeatability intraclass correlation coefficients exceeded 0.89 and 0.90, respectively.

CONCLUSIONS: It is possible to use MRI to identify the volume of interest with the maximum anatomic cross section of the PVM belly while minimizing the inadvertent inclusion of adjacent PRM or ICM in that measurement.

The Middle Fossa Approach with Self-drilling Screws: a Novel Technique for BONEBRIDGE Implantation

Publication: J Otolaryngol Head Neck Surg. 2019 Jul 29;48(1):35. PMID: 31358057 | PDF

Authors: You P, Siegel LH, Kassam Z, Hebb M, Parnes L, Ladak HM, Agrawal SK.

Institution: Department of Otolaryngology-Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, London, Canada.

Abstract:

BACKGROUND: Bone conduction implants can be used in the treatment of conductive or mixed hearing loss. The BONEBRIDGE bone conduction implant (BB-BCI) is an active, transcutaneous device. BB-BCI implantation can be performed through either the transmastoid or retrosigmoid approach with their respective limitations. Here, we present a third, novel approach for BB-BCI implantation.

OBJECTIVE: Describe the detailed surgical technique of BB-BCI implantation through a middle fossa approach with self-drilling screws and present preliminary audiometric outcome data following this approach.

METHODS: A single institution, retrospective chart review was completed for patients implanted with the BB-BCI via the middle fossa approach. Preoperative planning and modelling were performed using 3D Slicer. Audiological testing was performed pre- and post-operatively following standard audiometric techniques.

RESULTS: Forty patients underwent BB-BCI implantation using the middle fossa approach. Modelling techniques allowed for implantation through the use of external landmarks, obviating the need for intraoperative image guidance. The surgical technique was refined over time through experience and adaptation. Mean follow-up was 29 months (range 3-71 months) with no surgical complications, favourable cosmesis, and expected audiometric outcomes. An average functional gain of 39.6 dB (± 14.7 SD) was found.

CONCLUSION: The middle fossa technique with self-drilling screws is a safe and effective option for BONEBRIDGE implantation. As a reference for other groups considering this approach, an annotated video has been included as a supplement to the study.

Screen capture of the 3D Slicer interface in Conventional view for preoperative planning of middle fossa approach to BONEBRIDGE implantation. Traditional axial, sagittal, and coronal views of a temporal bone CT are visible at the bottom of the screen. The BC-FMT is highlighted with a red outline on these slices, and a red fiducial marks the centre of the implant on the skin. Blue box = module drop down menu. Green box = option to select Transform selection to alternate between global versus regional transform. Purple box = option to add fiducials. F = digital fiducial


The Middle Fossa Approach with Self-drilling Screws: a Novel Technique for BONEBRIDGE Implantation

Publication: J Otolaryngol Head Neck Surg. 2019 Jul 29;48(1):35. PMID: 31358057 | PDF

Authors: You P, Siegel LH, Kassam Z, Hebb M, Parnes L, Ladak HM, Agrawal SK.

Institution: Department of Otolaryngology-Head and Neck Surgery, Schulich School of Medicine & Dentistry, Western University, London, Canada.

Abstract:

BACKGROUND: Bone conduction implants can be used in the treatment of conductive or mixed hearing loss. The BONEBRIDGE bone conduction implant (BB-BCI) is an active, transcutaneous device. BB-BCI implantation can be performed through either the transmastoid or retrosigmoid approach with their respective limitations. Here, we present a third, novel approach for BB-BCI implantation.

OBJECTIVE: Describe the detailed surgical technique of BB-BCI implantation through a middle fossa approach with self-drilling screws and present preliminary audiometric outcome data following this approach.

METHODS: A single institution, retrospective chart review was completed for patients implanted with the BB-BCI via the middle fossa approach. Preoperative planning and modelling were performed using 3D Slicer. Audiological testing was performed pre- and post-operatively following standard audiometric techniques.

RESULTS: Forty patients underwent BB-BCI implantation using the middle fossa approach. Modelling techniques allowed for implantation through the use of external landmarks, obviating the need for intraoperative image guidance. The surgical technique was refined over time through experience and adaptation. Mean follow-up was 29 months (range 3-71 months) with no surgical complications, favourable cosmesis, and expected audiometric outcomes. An average functional gain of 39.6 dB (± 14.7 SD) was found.

CONCLUSION: The middle fossa technique with self-drilling screws is a safe and effective option for BONEBRIDGE implantation. As a reference for other groups considering this approach, an annotated video has been included as a supplement to the study.

Screen capture of the 3D Slicer interface in Conventional view for preoperative planning of middle fossa approach to BONEBRIDGE implantation. Traditional axial, sagittal, and coronal views of a temporal bone CT are visible at the bottom of the screen. The BC-FMT is highlighted with a red outline on these slices, and a red fiducial marks the centre of the implant on the skin. Blue box = module drop down menu. Green box = option to select Transform selection to alternate between global versus regional transform. Purple box = option to add fiducials. F = digital fiducial


Computed Tomographic Portography with Esophageal Variceal Measurements in the Evaluation of Esophageal Variceal Severity and Assessment of Esophageal Variceal Volume Efficacy

Publication: Acad Radiol. 2019 Jul 11. PMID: 31303576

Authors: Wan S, Wei Y, Yu H, Li Y, Yao S, Song B.

Institution: Department of Radiology, West China Hospital of Sichuan University, Chengdu, Sichuan, China.

Abstract:

RATIONALE AND OBJECTIVES: The aim of our study is to evaluate the severity of esophageal varices (EV), based on the computed tomographic portography (CTP) measurement of EV in the distal esophagus and to assess the prediction value of EV volume.

PATIENTS AND METHODS: A total of 53 EV patients examined by CTP within 4 weeks of upper endoscopy were evaluated, the patients were divided into a nonconspicuous EV group (mild-to-moderate EV, n = 28) and a conspicuous EV group (severe EV, n = 25) according to endoscopy results. The diameter, cross-sectional surface area (CSA), and volume of EV were measured independently using 3D Slicer by two experienced abdominal radiologists blinded to endoscopy findings. The averaged values measured by the two observers were used in the final dataset, these indicators' predictive performances were studied by using receiver operating characteristic curve analysis, and the area under the curve (Az) and the cutoff values were calculated to distinguish mild-to-moderate from severe EV.

RESULTS: The Az values of volume, diameter and CSA in differentiating severe EV were 0.817, 0.794, and 0.784 for observer-1, corresponding values for observer-2 were 0.796, 0.774, and 0.707, there was almost perfect interobserver agreement for all measurements. All indices were larger in the conspicuous group than the nonconspicuous group in both observers (p ≤ 0.01). In the final dataset, application of a 654.0-mm3-volume criterion yielded sensitivity, specificity of 96%, 50%, application of a 5.2-mm-diameter criterion yielded sensitivity, specificity of 80%, 75%, and application of a 68.6-mm2-CSA criterion yielded sensitivity, specificity of 52%, 93%.

CONCLUSION: The volume of EV could be used as a new effective indictor for evaluating EV, and use of volume, diameter, and CSA of EV based on CTP allows discrimination between mild-to-moderate and severe EV in cirrhotic patients.

Intracranial Mirror Aneurysm: Epidemiology, Rupture Risk, New Imaging, Controversies, and Treatment Strategies

Publication: World Neurosurg. 2019 Jul;127:165-175 PMID: 30954748

Authors: Liu HJ, Zhou H, Lu DL, Jiao YB, Chen SF, Cheng J, Yao XJ, Ren JY, Li SF, Liu W, Gao JC, Yue Y, Xu JX, Zhang PN, Feng YG.

Institution: Qingdao University, Qingdao, China.

Abstract:

There are some controversies about the surgical treatment strategy of mirror aneurysms. Whether to choose 1-stage or 2-stage surgery, bilateral or unilateral craniotomy, or surgical or interventional treatment are the main points in dispute. In this review, the different surgery strategies faced by patients are discussed. Different surgical methods are adopted based on the patient's individual state and the location and size of the aneurysm. A new imaging method is introduced using 3D Slicer, which clearly recognizes the relationship among aneurysm, brain tissue, skull, and nerve. The 3D Slicer can help surgeons undertake adequate preoperative preparation. In addition, we also introduce some ruptured factors (e.g., age, gender, hypertension, morphologic, and hemodynamic) concerning mirror aneurysm. Systematic discussion of the controversies and methods in surgical treatment of mirror aneurysms may provide new perspectives in future research for the prevention and treatment of mirror aneurysms.

Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows

Publication: J Digit Imaging. 2019 Jun;32(3):521-33. PMID: 30402669

Authors: Taveira LFR, Kurc T, Melo ACMA, Kong J, Bremer E, Saltz JH, Teodoro G.

Institution: Department of Computer Science, University of Brasília, Brasília, Brazil.

Abstract: We propose a software platform that integrates methods and tools for multi-objective parameter auto-tuning in tissue image segmentation workflows. The goal of our work is to provide an approach for improving the accuracy of nucleus/cell segmentation pipelines by tuning their input parameters. The shape, size, and texture features of nuclei in tissue are important biomarkers for disease prognosis, and accurate computation of these features depends on accurate delineation of boundaries of nuclei. Input parameters in many nucleus segmentation workflows affect segmentation accuracy and have to be tuned for optimal performance. This is a time-consuming and computationally expensive process; automating this step facilitates more robust image segmentation workflows and enables more efficient application of image analysis in large image datasets. Our software platform adjusts the parameters of a nuclear segmentation algorithm to maximize the quality of image segmentation results while minimizing the execution time. It implements several optimization methods to search the parameter space efficiently. In addition, the methodology is developed to execute on high-performance computing systems to reduce the execution time of the parameter tuning phase. These capabilities are packaged in a Docker container for easy deployment and can be used through a friendly interface extension in 3D Slicer. Our results using three real-world image segmentation workflows demonstrate that the proposed solution is able to (1) search a small fraction (about 100 points) of the parameter space, which contains billions to trillions of points, and improve the quality of segmentation output by × 1.20, × 1.29, and × 1.29, on average; (2) decrease the execution time of a segmentation workflow by up to 11.79× while improving output quality; and (3) effectively use parallel systems to accelerate parameter tuning and segmentation phases.

Funding:

  • R01 LM011119/U.S. National Library of Medicine
  • U24 CA180924/National Cancer Institute
  • R01 LM009239/U.S. National Library of Medicine
  • K25 CA181503/National Institutes of Health
  • UG3 CA225021/CA/NCI NIH HHS/United States

In vivo Localization of Cortical Areas using a 3D Computerized Atlas of the Marmoset Brain

Publication: Brain Struct Funct. 2019 Jun;224(5):1957-69. PMID: 30963231

Authors: Risser L, Sadoun A, Mescam M, Strelnikov K, Lebreton S, Boucher S, Girard P, Vayssière N, Rosa MGP, Fonta C.

Institution: Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS IMT, 31062, Toulouse Cedex 9, France.

Abstract: We created a volumetric template of the marmoset (Callithrix jacchus) brain, which enables localization of the cortical areas defined in the Paxinos et al. (The marmoset brain in stereotaxic coordinates. Elsevier Academic Press, Cambridge, 2012) marmoset brain atlas, as well as seven broader cortical regions (occipital, temporal, parietal, prefrontal, motor, limbic, insular), different brain compartments (white matter, gray matter, cerebro-spinal fluid including ventricular spaces), and various other structures (brain stem, cerebellum, olfactory bulb, hippocampus). The template was designed from T1-weighted MR images acquired using a 3 T MRI scanner. It was based on a single fully segmented marmoset brain image, which was transported onto the mean of 13 adult marmoset brain images using a diffeomorphic strategy that fully preserves the brain topology. In addition, we offer an automatic segmentation pipeline which fully exploits the proposed template. The segmentation pipeline was quantitatively assessed by comparing the results of manual and automated segmentations. An associated program, written in Python, can be used from a command-line interface, or used interactively as a module of the 3D Slicer software. This program can be applied to the analysis of multimodal images, to map specific cortical areas in lesions or to define the seeds for further tractography analyses.

Ancient Machine Tools for the Construction of the Antikythera Mechanism Parts

Publication: Digital Applications in Archaeology and Cultural Heritage. 2019 Jun; 13:e00092.

Authors: Aristeidis Voulgaris, Christophoros Mouratidis, Andreas Vossinakis.

Institution: Thessaloniki Astronomy Club, Thessaloniki, Greece.

Abstract: The present work deals with the study, design, original reconstruction and use of the bow drill of the late archaic period (ca 490 BC), as depicted in two different red figure vases and the vertical lathe depicted on an engraved wall painting of the Petosiris tomb of the Ptolemaic era (300 BC). After the reconstruction of the three ancient tools, during the implementation of the FRAMe Project, their use was thoroughly studied, from which useful conclusions were drawn about the material processing in antiquity, as well as the details of the construction of the Antikythera Mechanism components. Following the new findings detected from the authors’ study of the X-Ray Computed Tomographies from Antikythera Mechanism Research Project, these ancient machine tools can be considered as the progenitors of the Hellenistic period machine tools, which were used for the construction of the mechanical components of the Mechanism.

Comprehensive Review of 3D Segmentation Software Tools for MRI Usable for Pelvic Surgery Planning

Publication: J Digit Imaging. 2019 Jun 24. PMID: 31236743

Authors: Virzì A, Muller CO, Marret JB, Mille E, Berteloot L, Grévent D, Boddaert N, Gori P, Sarnacki S, Bloch I.

Institution: LTCI, Télécom Paris, Institut Polytechnique de Paris, Paris, France.

Abstract:

Patient-specific 3D modeling is the first step towards image-guided surgery, the actual revolution in surgical care. Pediatric and adolescent patients with rare tumors and malformations should highly benefit from these latest technological innovations, allowing personalized tailored surgery. This study focused on the pelvic region, located at the crossroads of the urinary, digestive, and genital channels with important vascular and nervous structures. The aim of this study was to evaluate the performances of different software tools to obtain patient-specific 3D models, through segmentation of magnetic resonance images (MRI), the reference for pediatric pelvis examination. Twelve software tools freely available on the Internet and two commercial software tools were evaluated using T2-w MRI and diffusion-weighted MRI images. The software tools were rated according to eight criteria, evaluated by three different users: automatization degree, segmentation time, usability, 3D visualization, presence of image registration tools, tractography tools, supported OS, and potential extension (i.e., plugins). A ranking of software tools for 3D modeling of MRI medical images, according to the set of predefined criteria, was given. This ranking allowed us to elaborate guidelines for the choice of software tools for pelvic surgical planning in pediatric patients. The best-ranked software tools were Myrian Studio, ITK-SNAP, and 3D Slicer, the latter being especially appropriate if nerve fibers should be included in the 3D patient model. To conclude, this study proposed a comprehensive review of software tools for 3D modeling of the pelvis according to a set of eight criteria and delivered specific conclusions for pediatric and adolescent patients that can be directly applied to clinical practice.

New, Simple and Reliable Volumetric Calculation Technique in Incisional Hernias with Loss of Domain=

Publication: Hernia. 2019 Jun 19. PMID: 31218439

Authors: Martre P, Sarsam M, Tuech JJ, Coget J, Schwarz L, Khalil H.

Institution: Department of Digestive Surgery, Rouen University Hospital, Rouen, France.

Abstract:

INTRODUCTION: The management of hernias with loss of domain is a challenging problem. It has been shown that the volume of the incisional hernia/peritoneal volume ratio < 20% was a predictive factor for tension-free fascia closure, after pre-operative pneumoperitoneum preparation (Goni Moreno technique). In this study, we propose an easy, reliable and fast technique to perform volumetric calculation, by the surgeon alone.

MATERIALS AND METHODS: 3D Slicer software (free open-source software) was used to calculate with precision the intra-peritoneal and intra-hernia volumes, and to create a 3D reconstruction of both volumes. The measurement technique is described step by step using detailed figures and videos.

RESULTS: The method was used to calculate the volumes for five consecutive patients, managed between January 2018 and March 2019. All the five patients had a ratio greater than 20% and, therefore, received a PPP program. The effectiveness of the procedure is objectified by the increase of the intraabdominal volume and the reduction of the incisional hernia/peritoneal volume ratio. The feasibility of a tension-free fascia closure was confirmed for the five patients.

CONCLUSION: In addition to a standardized definition of "loss of domain", a standardized volumetric technique, easy to reproduce, needs to be adopted. Our method can be done by any surgeon with basic computer skills and radiological knowledge in an autonomous and a fast manner, thus helping to select the right technique for the right patient.

Three-dimensional Neuronavigation in SEEG-guided Epilepsy Surgery

Publication: Acta Neurochir (Wien). 2019 May;161(5):917-23. PMID: 30937608

Authors: Minkin K, Gabrovski K, Sirakov S, Penkov M, Todorov Y, Karakostov V, Dimova P.

Institution: Department of Neurosurgery, University Hospital "Saint Ivan Rilski", Sofia, Bulgaria.

Abstract: OBJECTIVES: Epilepsy surgery is mainly cortical surgery and the precise definition of the epileptogenic zone on the complex cortical surface is of paramount importance. Stereoelectroencephalography (SEEG) may delineate the epileptogenic zone even in cases of non-lesional epilepsy. The aim of our study was to present a technique of 3D neuronavigation based on the brain surface and SEEG electrodes reconstructions using FSL and 3D Slicer software.

PATIENTS AND METHODS: Our study included 26 consecutive patients operated on for drug-resistant epilepsy after SEEG exploration between January 2015 and December 2017. All patients underwent 1.5 T pre-SEEG MRI, post-SEEG CT, DICOM data post-processing using FSL and 3D Slicer, preoperative planning on 3D Slicer, and intraoperative 3D neuronavigation. Accuracy and precision of 3D SEEG reconstruction and 3D neuronavigation was assessed.

RESULTS: We identified 125 entry points of SEEG electrodes during 26 operations. The accuracy of 3D reconstruction was 0.8 mm (range, 0-2 mm) with a precision of 1.5 mm. The accuracy of 3D SEEG neuronavigation was 2.68 mm (range, 0-6 mm). The precision of 3D neuronavigation was 1.48 mm.

CONCLUSION: 3D neuronavigation for SEEG-guided epilepsy surgery using free software for post-processing of common MRI sequences is possible and a reliable method even with navigation systems without a brain extraction tool.

Complete Thoracolumbar Fracture-dislocation with Intact Neurologic Function: Explanation of a Novel Cord Saving Mechanism

Publication: J Spinal Cord Med. 2018 May;41(3):367-76. PMID: 28648115 | PDF

Authors: Rahimizadeh A, Asgari N, Rahimizadeh A.

Institution: Department of Neurosurgery, Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Iran University of Medical Science, Tehran, Iran.

Abstract:

BACKGROUND: The thoracolumbar junction from T11 to L2 is a common site of injury in which fracture and dislocations are the most prevalent ones occurring at this location. Fracture dislocation is defined as failure of all three columns of the spine with gross displacement. Considering the significant violence necessary to produce fracture dislocations, these injuries are often associated with major neural deficit, with the majority of casualties becoming paraplegic immediately. Preservation of neurological function following complete fracture dislocation is quite rare entity.

OBJECTIVE: To represent the possibility of existence of a preservation mechanism for functional integrity of cord despite spinal gross fracture dislocation by reproducing the injury on a plastic model and simulating a corresponding model using 3D Slicer software, detailed description the pathomechanism of neurologic sparing.

CASE REPORT: A 19-year-old female who sustained severe thoracolumbar fracture dislocation but with normal neurology is presented. Despite the severity of the condition, the diagnosis was initially missed due to associated vital injuries.

RESULTS: Combined posterior and anterior surgery resulted in optimal coronal and sagittal alignment, as well as proper stabilization without any complication. At 9-year follow-up, the patient was found to be doing well.

CONCLUSION: The prognosis for complete recovery with preplanned surgical intervention in thoracolumbar injuries affecting all three columns but with normal neurologic function is promising based on images, plastic models and 3D simulated model based on digital images.

Virtual Reconstruction of Paranasal Sinuses from CT Data: A Feasibility Study for Forensic Application

Publication: Diagn Interv Imaging. 2019 Mar;100(3):163-8. PMID: 30553743

Authors: Gach P, Tuchtan-Torrents L, Delteil C, Adalian P, Piercecchi MD, Ebert LC, Gorincour G.

Institution: LiiE, EA 4264, CERIMED, Aix-Marseille University, 13005 Marseille, France.

Abstract: PURPOSE: The purpose of this study was to report the feasibility of computed modelization and reconstitution of the paranasal sinuses, before and after trauma, from CT data.

MATERIALS AND METHODS: We modeled and reconstructed the paranasal sinuses of two patients (A and B), before and after trauma, using two different softwares (3D Slicer and Blender®). Both patients had different numbers and locations of fractures. The 3D Slicer software was used to create a 3D model from CT data. We then imported the 3D data into the Blender® software, to reconstruct and compare the dimensions of the paranasal sinuses before and after trauma.

RESULTS: The 3 fragments of patient A and the 7 fragments of patient B could be repositioned in the pre-traumatic configuration. Distance measurements proved to be similar between pre- and post-traumatic 3D volumes.

CONCLUSION: After simple trauma, bone facial anatomy reconstruction is manually feasible. The whole procedure could benefit from automatization through machine learning. However, this feasibility must be confirmed on more severely fractured paranasal sinuses, to consider an application in forensic identification.

Real-Time Adaptive Planning Method for Radiotherapy Treatment Delivery for Prostate Cancer Patients, Based on a Library of Plans Accounting for Possible Anatomy Configuration Changes

Publication: PLoS One. 2019 Feb 28;14(2):e0213002. PMID: 30818345 | PDF

Authors: Antico M, Prinsen P, Cellini F, Fracassi A, Isola AA, Cobben D, Fontanarosa D.

Institution: School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, Queensland, Australia.

Abstract: BACKGROUND AND PURPOSE: In prostate cancer treatment with external beam radiation therapy (EBRT), prostate motion and internal changes in tissue distribution can lead to a decrease in plan quality. In most currently used planning methods, the uncertainties due to prostate motion are compensated by irradiating a larger treatment volume. However, this could cause underdosage of the treatment volume and overdosage of the organs at risk (OARs). To reduce this problem, in this proof of principle study we developed and evaluated a novel adaptive planning method. The strategy proposed corrects the dose delivered by each beam according to the actual position of the target in order to produce a final dose distribution dosimetrically as similar as possible to the prescribed one.

MATERIAL AND METHODS: Our adaptive planning method was tested on a phantom case and on a clinical case. For the first, a pilot study was performed on an in-silico pelvic phantom. A "library" of intensity modulated RT (IMRT) plans corresponding to possible positions of the prostate during a treatment fraction was generated at planning stage. Then a 3D random walk model was used to simulate possible displacements of the prostate during the treatment fraction. At treatment stage, at the end of each beam, based on the current position of the target, the beam from the library of plans, which could reproduce the best approximation of the prescribed dose distribution, was selected and delivered. In the clinical case, the same approach was used on two prostate cancer patients: for the first a tissue deformation was simulated in-silico and for the second a cone beam CT (CBCT) taken during the treatment was used to simulate an intra-fraction change. Then, dosimetric comparisons with the standard treatment plan and, for the second patient, also with an isocenter shift correction, were performed. "...The CT was then elastically deformed on the CBCT using the B-spline method in 3D Slicer."

RESULTS: For the phantom case, the plan generated using the adaptive planning method was able to meet all the dosimetric requirements and to correct for a misdosage of 13% of the dose prescription on the prostate. For the first clinical case, the standard planning method caused underdosage of the seminal vesicles, respectively by 5% and 4% of the prescribed dose, when the position changes for the target were correctly taken into account. The proposed adaptive planning method corrected any possible missed target coverage, reducing at the same time the dose on the OARs. For the second clinical case, both with the standard planning strategy and with the isocenter shift correction target coverage was significantly worsened (in particular uniformity) and some organs exceeded some toxicity objectives. While with our approach, the most uniform coverage for the target was produced and systematically the lowest toxicity values for the organs at risk were achieved.

CONCLUSIONS: In our proof of principle study, the adaptive planning method performed better than the standard planning and the isocenter shift methods for prostate EBRT. It improved the coverage of the treatment volumes and lowered the dose to the OARs. This planning method is particularly promising for hypofractionated IMRT treatments in which a higher precision and control on dose deposition are needed. Further studies will be performed to test more extensively the proposed adaptive planning method and to evaluate it at a full clinical level.

Isodose lines for two pelvic slices
In the top and the bottom figure a, b, c and d correspond respectively to the PTV planning method without/with intra-fraction motion and the adaptive planning method with/without MU rescaling (both with intra-fraction motion). In the top figure in a and b the PTV is shown as a grey shaded area surrounding the prostate. The prostate is visible only in the slice shown in the top figure.
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Unique Metasomal Musculature in Sweat Bees (Hymenoptera, Apoidea, Halictidae) Revealed by Micro-CT Scanning

Publication: American Museum Novitates 2019 Feb; 3920:28 | PDF

Authors: Herhold, Hollister W.; Davis, Steven R.; Smith, Corey Shepard.; Engel, Michael S.; Grimaldi, David A.

Institution: American Museum of Natural History, New York, NY

Abstract: Bees of the family Halictidae (Apoidea: Anthophila) have three pairs of thick, bundled muscles that are circular to subcircular in cross section within the first metasomal segment, as revealed by micro-CT scanning of 16 species in 15 genera of five bee families. In nonhalictids and the basal halictid subfamily Rophitinae, these muscles are planar (flat and sheetlike), typically lying between the anterior air sacs and abdominal wall. In Nomiinae and Halictinae, these muscles, especially the dorsal-ventral pair, bulge into air-sac space, partly enveloped by air-sac membrane. A possible function may be to facilitate metasomal compression and contraction, and thus air flow. The bundled shape of these derived halictid muscles is similar to that of flight muscles, but further data is needed to determine if they are fibrillar, which would suggest a completely different function. "Segmentation and volume rendering was done using 3D Slicer v4.9."

Volume rendering of Lasioglossum (Dialictus) sp. (Halictinae: Halictini), showing location of abdominal air sacs, displayed as a yellow solid, and “grooves” where metasomal muscles extend into the air-sac space. The insect’s exoskeleton and internal anatomy is rendered translucent, allowing examination of air-sac morphology. The bilateral asymmetry shown here is not uncommon, and usually has to do with how recently the specimen has fed. Distension of the gut can occupy space normally taken up by air sacs.
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3D Reconstruction of MR-Visible Fe3O4-Mesh Implants: Pelvic Mesh Measurement Techniques and Preliminary Findings

Publication: Neurourol Urodyn. 2019 Jan;38(1):369-78. PMID: 30387537 | |PDF

Authors: Brocker KA, Mokry T, Alt CD, Kauczor HU, Lenz F, Sohn C, DeLancey JO, Chen L.

Institution: Department of Obstetrics and Gynecology, Medical School, University of Heidelberg, Heidelberg, Germany.

Abstract: AIMS: To develop MR-based measurement technique to evaluate the postoperative dimension and location of implanted magnetic resonance (MR)-visible meshes.

METHODS: This technique development study reports findings of six patients (A-F) with cystoceles treated with anterior vaginal MR-visible Fe3O4 -polypropylene implants. Implanted meshes were reconstructed from 3 months and/or 1 year postsurgical MR-images using 3D Slicer. Measurements including mesh length, distance to the ischial spines, pudendal, and obturator neurovascular bundles and urethra were obtained using software Rhino® and a custom Matlab® program. The range of implanted mesh length and their placements were reported and compared with mesh design and implantation recommendations. With the anterior/posterior-mesh-segment-ratio mesh shrinkage localization was evaluated.

RESULTS: Examinations were possible for patients A-D 3 months and for A, C, E, and F 1 year postsurgical. The mesh was at least 40% shorter in all patients 3 months and/or 1 year postoperatively. A, B showed shrinkage in the anterior segment, D, E in the posterior segment (Patients C, F not applicable due to intraoperative mesh trimming). Patient E presented pain in the area of mesh shrinkage. In Patient C posterior mesh fixations were placed in the iliococcygeal muscle rather than sacrospinous ligaments. Arm placement less than 20 mm from the pudendal neurovascular bundles was seen in all cases. The portion of the urethra having mesh underneath it ranged from 19% to 55%.

CONCLUSIONS: MRI-based measurement techniques have been developed to quantify implanted mesh location and dimension. Mesh placement variations possibly correlating with postoperative complications can be illustrated.

Funding:

  • P50 HD044406/HD/NICHD NIH HHS/United States
  • R21 HD079908/HD/NICHD NIH HHS/United States

A Complete Workflow for Utilizing Monte Carlo Toolkits in Clinical Cases for a Double-Scattering Proton Therapy System

Publication: J Appl Clin Med Phys. 2019 Jan;20(1):23-30. PMID: 30426669 | PDF

Authors: Muller L, Prusator M, Ahmad S, Chen Y.

Institution: Department of Radiation Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK.

Abstract: The methods described in this paper allow end users to utilize Monte Carlo (MC) toolkits for patient-specific dose simulation and perform analysis and plan comparisons for double-scattering proton therapy systems. The authors aim to fill two aspects of this process previously not explicitly published. The first one addresses the modeling of field-specific components in simulation space. Patient-specific compensator and aperture models are exported from treatment planning system and converted to STL format using a combination of software tools including Matlab and Autodesk's Netfabb. They are then loaded into the MC geometry for simulation purpose. The second details a method for easily visualizing and comparing simulated doses with the dose calculated from the treatment planning system. This system is established by utilizing the open source software 3D Slicer. The methodology was demonstrated with a two-field proton treatment plan on the IROC lung phantom. Profiles and two-dimensional (2D) dose planes through the target isocenter were analyzed using our in-house software tools. This present workflow and set of codes can be easily adapted by other groups for their clinical practice.

Morphological Analysis of Sigmoid Sinus Anatomy: Clinical Applications to Neurotological Surgery

Publication: J Otolaryngol Head Neck Surg. 2019 Jan 11;48(1):2. PMID: 30635049 | PDF

Authors: Van Osch K, Allen D, Gare B, Hudson TJ, Ladak H, Agrawal SK.

Institution: Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada.

Abstract: OBJECTIVES: The primary objective of this study was to use high-resolution micro-CT images to create accurate three-dimensional (3D) models of several intratemporal structures, and to compare several surgically important dimensions within the temporal bone. The secondary objective was to create a statistical shape model (SSM) of a dominant and non-dominant sigmoid sinus (SS) to provide a template for automated segmentation algorithms.

METHODS: A free image processing software, 3D Slicer, was utilized to create three-dimensional reconstructions of the SS, jugular bulb (JB), facial nerve (FN), and external auditory canal (EAC) from micro-CT scans. The models were used to compare several clinically important dimensions between the dominant and non-dominant SS. Anatomic variability of the SS was also analyzed using SSMs generated using the Statismo software framework.

RESULTS: Three-dimensional models from 38 temporal bones were generated and analyzed. Right dominance was observed in 74% of the paired SSs. All distances were significantly shorter on the dominant side (p < 0.05), including: EAC - SS (dominant: 13.7 ± 3.4 mm; non-dominant: 15.3 ± 2.7 mm), FN - SS (dominant: 7.2 ± 1.8 mm; non-dominant: 8.1 ± 2.3 mm), 2nd genu FN - superior tip of JB (dominant: 8.7 ± 2.2 mm; non-dominant: 11.2 ± 2.6 mm), horizontal distance between the superior tip of JB - descending FN (dominant: 9.5 ± 2.3 mm; non-dominant: 13.2 ± 3.5 mm), and horizontal distance between the FN at the stylomastoid foramen - JB (dominant: 5.4 ± 2.2 mm; non-dominant: 7.7 ± 2.1). Analysis of the SSMs indicated that SS morphology is most variable at its junction with the transverse sinus, and least variable at the JB.

CONCLUSIONS: This is the first known study to investigate the anatomical variation and relationships of the SS using high resolution scans, 3D models and statistical shape analysis. This analysis seeks to guide neurotological surgical approaches and provide a template for automated segmentation and surgical simulation.

"In 3D Slicer, nine fiducials (F1 – F9) were placed on the 3D reconstructions of the SS, JB, EAC, and FN to analyze several surgically relevant relationships between these structures."

Funding:

  • 381117/Collaborative Health Research Projects
Fiducials and distances calculated from coordinates (BLUE - SS, YELLOW - FN, PURPLE - EAC). a. EAC – SS (F1 – F2); Descending FN – SS (F3 – F4). b. 2nd genu FN – Superior tip JB. (F5 – F6); Descending FN - Superior tip JB (F6 – F7); FN at the SMF - JB (F8 – F9).
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