Difference between revisions of "Main Page/SlicerCommunity/2022"

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'''Abstract:''' Four-dimensional data sets are increasingly common in MRI and CT. While clinical visualization often focuses on individual temporal phases capturing the tissue(s) of interest, it may be possible to gain additional insight through exploring animated 3D reconstructions of physiological motion made possible by augmented or virtual reality representations of 4D patient imaging. Cardiac CT acquisitions can provide sufficient spatial resolution and temporal data to support advanced visualization, however, there are no open-source tools readily available to facilitate the transformation from raw medical images to dynamic and interactive augmented or virtual reality representations. To address this gap, we developed a workflow using free and open-source tools to process 4D cardiac CT imaging starting from raw DICOM data and ending with dynamic AR representations viewable on a phone, tablet, or computer. In addition to assembling the workflow using existing platforms ([http://www.slicer.org '''3D Slicer'''] and Unity), we also contribute two new features: 1. custom software which can propagate a segmentation created for one cardiac phase to all others and export to surface files in a fully automated fashion, and 2. a user interface and linked code for the animation and interactive review of the surfaces in augmented reality. Validation of the surface-based areas demonstrated excellent correlation with radiologists' image-based areas (R > 0.99). While our tools were developed specifically for 4D cardiac CT, the open framework will allow it to serve as a blueprint for similar applications applied to 4D imaging of other tissues and using other modalities. We anticipate this and related workflows will be useful both clinically and for educational purposes.
'''Abstract:''' Four-dimensional data sets are increasingly common in MRI and CT. While clinical visualization often focuses on individual temporal phases capturing the tissue(s) of interest, it may be possible to gain additional insight through exploring animated 3D reconstructions of physiological motion made possible by augmented or virtual reality representations of 4D patient imaging. Cardiac CT acquisitions can provide sufficient spatial resolution and temporal data to support advanced visualization, however, there are no open-source tools readily available to facilitate the transformation from raw medical images to dynamic and interactive augmented or virtual reality representations. To address this gap, we developed a workflow using free and open-source tools to process 4D cardiac CT imaging starting from raw DICOM data and ending with dynamic AR representations viewable on a phone, tablet, or computer. In addition to assembling the workflow using existing platforms ([http://www.slicer.org '''3D Slicer'''] and Unity), we also contribute two new features: 1. custom software which can propagate a segmentation created for one cardiac phase to all others and export to surface files in a fully automated fashion, and 2. a user interface and linked code for the animation and interactive review of the surfaces in augmented reality. Validation of the surface-based areas demonstrated excellent correlation with radiologists' image-based areas (R > 0.99). While our tools were developed specifically for 4D cardiac CT, the open framework will allow it to serve as a blueprint for similar applications applied to 4D imaging of other tissues and using other modalities. We anticipate this and related workflows will be useful both clinically and for educational purposes.
==Three-Dimensional Evaluation of Maxillary Second Molar Position in Untreated Patients With Normal Occlusion: Implications for Preadjusted Appliance Prescriptions==
{| width="100%"
'''Publication:''' [https://www.ncbi.nlm.nih.gov/pubmed/33783560 J Orofac Orthop. 2021 Mar 30. PMID: 33783560]
'''Authors:''' Goracci C, Ruellas AC, Nieri M, Crouch S, McNamara JA Jr, Franchi L.
'''Institution:''' Department of Medical Biotechnologies, University of Siena, Policlinico Le Scotte, Siena, Italy.
'''Abstract:''' A sample of 41 subjects (16 females, 25 males) was selected from the University of Michigan Growth Study (UMGS). Digital dental casts with fully erupted second molars in occlusion were chosen (mean age 14.9 ± 1.3 years). Digital measurements were recorded with the open source software [http://www.slicer.org '''3D Slicer''']. The digital measurements of the UMGS sample were compared with the manual measurements collected by Andrews from his sample of untreated class I subjects with normal overbite and overjet. Two mixed effect models (sagittal and transversal inclinations) were performed. The "random effect" was represented by the subjects, while the "fixed effects" were the two compared groups, the side of the arch (right and left), and the group × side interaction. Outcome variables were sagittal and transversal inclinations of the upper second molars.

Revision as of 22:09, 1 June 2022

Home < Main Page < SlicerCommunity < 2022

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The community that relies on 3D Slicer is large and active: (numbers below updated on November 1st, 2022)

  • 1,623+ 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 2022

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.



Comparison of Response Assessment in Veterinary Neuro-Oncology and Two Volumetric Neuroimaging Methods to Assess Therapeutic Brain Tumour Responses in Veterinary Patients

Publication: Vet Comp Oncol. 2022 Jun;20(2):404-415. PMID: 34792828

Authors: Coppola G, Morris J, Gutierrez-Quintana R, Burnside S, José-López R.

Institution: School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

Abstract: Standardized veterinary neuroimaging response assessment methods for brain tumours are lacking. Consequently, a response assessment in veterinary neuro-oncology (RAVNO) system which uses the sum product of orthogonal lesion diameters on 1-image section with the largest tumour area, has recently been proposed. In this retrospective study, 22 pre-treatment magnetic resonance imaging (MRI) studies from 18 dogs and four cats with suspected intracranial neoplasia were compared by a single observer to 32 post-treatment MRIs using the RAVNO system and two volumetric methods based on tumour margin or area delineation with HOROS and 3D Slicer software, respectively. Intra-observer variability was low, with no statistically significant differences in agreement index between methods (mean AI ± SD, 0.91 ± 0.06 for RAVNO; 0.86 ± 0.08 for HOROS; and 0.91 ± 0.05 for 3D Slicer), indicating good reproducibility. Response assessments consisting of complete or partial responses, and stable or progressive disease, agreed in 23 out of 32 (72%) MRI evaluations using the three methods. The RAVNO system failed to identify changes in mass burden detected with volumetric methods in six cases. 3D Slicer differed from the other two methods in three cases involving cysts or necrotic tissue as it allowed for more accurate exclusion of these structures. The volumetric response assessment methods were more precise in determining changes in absolute tumour burden than RAVNO but were more time-consuming to use. Based on observed agreement between methods, low intra-observer variability and decreased time constraint, RAVNO might be a suitable response assessment method for the clinical setting.

Intracardiac MR Imaging (ICMRI) Guiding-Sheath With Amplified Expandable-Tip Imaging and MR-Tracking for Navigation and Arrythmia Ablation Monitoring: Swine Testing at 1.5 and 3T

Publication: Magn Reson Med. 2022 Jun;87(6):2885-2900. PMID: 35142398

Authors: Schmidt EJ, Olson G, Tokuda J, Alipour A, Watkins RD, Meyer EM, Elahi H, Stevenson WG, Schweitzer J, Dumoulin CL, Johnson T, Kolandaivelu A, Loew W, Halperin HR.

Institution: Medicine (Cardiology), Johns Hopkins University, Baltimore, MD, USA.

Abstract: Purpose: Develop a deflectable intracardiac MR imaging (ICMRI) guiding-sheath to accelerate imaging during MR-guided electrophysiological (EP) interventions for radiofrequency (500 kHz) ablation (RFA) of arrythmia. Requirements include imaging at three to five times surface-coil SNR in cardiac chambers, vascular insertion, steerable-active-navigation into cardiac chambers, operation with ablation catheters, and safe levels of MR-induced heating.

Methods: ICMRI's 6 mm outer-diameter (OD) metallic-braided shaft had a 2.6 mm OD internal lumen for ablation-catheter insertion. Miniature-Baluns (MBaluns) on ICMRI's 1 m shaft reduced body-coil-induced heating. Distal section was a folded "star"-shaped imaging-coil mounted on an expandable frame, with an integrated miniature low-noise-amplifier overcoming cable losses. A handle-activated movable-shaft expanded imaging-coil to 35 mm OD for imaging within cardiac-chambers. Four MR-tracking micro-coils enabled navigation and motion-compensation, assuming a tetrahedron-shape when expanded. A second handle-lever enabled distal-tip deflection. ICMRI with a protruding deflectable EP catheter were used for MR-tracked navigation and RFA using a dedicated 3D Slicer user-interface. ICMRI was tested at 3T and 1.5T in swine to evaluate (a) heating, (b) cardiac-chamber access, (c) imaging field-of-view and SNR, and (d) intraprocedural RFA lesion monitoring.

Results: The 3T and 1.5T imaging SNR demonstrated >400% SNR boost over a 4 × 4 × 4 cm3 FOV in the heart, relative to body and spine arrays. ICMRI with MBaluns met ASTM/IEC heating limits during navigation. Tip-deflection allowed navigating ICMRI and EP catheter into atria and ventricles. Acute-lesion long-inversion-time-T1-weighted 3D-imaging (TWILITE) ablation-monitoring using ICMRI required 5:30 min, half the time needed with surface arrays alone.

Conclusion: ICMRI assisted EP-catheter navigation to difficult targets and accelerated RFA monitoring.

New Ultra-Fast Algorithm for Cochlear Implant Misalignment Detection

Publication: Eur J Radiol. 2022 Jun;151:110283. PMID: 35390602.

Authors: Waldeck S, Helal R, Al-Dhamari I, Schmidt S, von Falck C, Chapot R, Brockmann M, Overhoff D.

Institution: Department of Diagnostic and Interventional Radiology and Neuroradiology, Bundeswehr Central Hospital Koblenz, Germany.

Abstract: Purpose: Postoperative imaging following cochlear implant (CI) placement is currently the only means of diagnosing proper electrode position. Manual multiplanar reconstruction (MPR) analysis of CT and CBCT is time-consuming and requires extensive training. This study aims to evaluate the rate of CI misalignment and to determine the amount of time necessary to reach a diagnosis of correct versus incorrect CI placement for readers of different experience levels, using a novel algorithm for image analysis (ACIR) compared to MPR analysis.

Method: The retrospective single centre study included 333 patients with cochlear implant surgery between May 2002 and May 2021. Postoperative CT and CBCT images were evaluated in three subgroups and the time to diagnosis was documented. Group 1: image evaluation using conventional MPR analysis; group 2: image evaluation by an experienced neuroradiologist via a novel ultra-fast algorithm; group 3: image evaluation by a young specialist via novel ultra-fast algorithm. T-test and Pearson's chi-squared test were used for inter-group comparisons.

Results: 333 patients (63.3 ± 15.9 years; 188 men) with 335 CIs were evaluated. The rate of CI misalignment diagnosed from 3D imaging was 14.3% (n = 48). MPR analysis required 255.7 ± 70.4 s per temporal bone, whereas 3D Slicer plugin reduced analysis time to 83.3 ± 7.7 s (p < 0.001) for the experienced reader and 89.6 ± 8.7 s for the young specialist (p < 0.001).

Conclusion: 3D postoperative imaging reveals high incidences of CI misalignment. Application of a novel ultra-fast algorithm significantly reduces the time for diagnosis compared to MPR analysis for readers of varying experience levels.

The Preoperative Evaluation Value of 3D-Slicer Program Before Microsurgical Vascular Decompression in Patients With Hemifacial Spasm

Publication: Clin Neurol Neurosurg. 2022 Jun;217:107241. PMID: 35429853.

Authors: Shi H, Li Y, Wang Y, Guo W, Zhang K, Du Y, Shi H, Qian T.

Institution: Department of Neurosurgery, Hebei General Hospital, Shijiazhuang, China.

Abstract: Background: To compare the diagnostic accuracy of 3D fast imaging employing steady-state acquisition (FIESTA) combined with 3D-time-of-flight (TOF) MR angiography (MRA) sequences (FTMS) and 3D-reconstuction synthesized by 3D Slicer program in evaluation the neurovascular relationships and offending vessels preoperatively in patients with hemifacial spasm (HFS).

Methods: Clinical data of HFS patients who underwent microsurgical vascular decompression (MVD) were analyzed. All patients underwent MRA scans with FTMS and 3D-reconstruction before surgery. The neurovascular relationship and offending vessels were evaluated and compared with intraoperative findings.

Results: Forty patients were included in this study, 18 (45%) of them were male. The mean age was 49.6 years. The Kappa identity tests identified the agreement between the FTMS and intraoperative findings in evaluating the neurovascular relationship and offending vessel was 0.263 and 0.643, respectively. The agreement between the 3D-reconstruction and intraoperative findings was 0.633 and 0.921 respectively. There was borderline significant difference between the two methods in predicting neurovascular relationship (χ2 = 9.363, P = 0.053), and there were significant differences between the two methods in predicting offending vessels (χ2 = 188.408, P < 0.001). The sensitivity and specificity of FTMS in evaluating the neurovascular relationship were 89.7% and 100%, respectively, while those with 3D-reconstruction were both 100%. Moreover, the correct 3D- reconstruction examinations in predicting vessel and nerve relationships (r = 0.634, P = 0.034) and offending vessels (r = 0.652, P = 0.028) were significantly correlated with completely symptoms remission.

Conclusions: The 3D-reconstuction synthesized by 3D Slicer program was more accurate than FTMS in preoperative evaluation of neurovascular relationship and offending vessel. The technique is expected to be helpful in preoperative evaluation.

Availability of data and material: The dataset used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Treatment of Pediatric Vaginal Rhabdomyosarcoma With the Use of a Real-Time Tracked Custom Applicator

Publication: Brachytherapy. May-Jun 2022;21(3):291-299. PMID: 35623721 | PDF

Authors: Morcos M, Vogel J, Garcia JR, Gomez-Lobo V, Bartolac S.

Institution: Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins Medicine, Baltimore, MD, USA.

Abstract: Purpose: To describe the development, design, and implementation of a 3D printed MR-compatible pediatric vaginal multichannel brachytherapy cylinder. Safety and quality measures to ensure consistent treatment required innovative identification on MR and CT, and real-time tracking.

Methods and materials: A 4-year-old with vaginal botryoides rhabdomyosarcoma underwent MR-simulation with a custom 3D printed biocompatible resin cylinder with four channels to ensure dose optimization capability. A total of four identifier regions were designed into the applicator in order to utilize these for MR-visualization and real-time tracking. A biocompatible 3D printed cylinder was designed to meet dose objectives using an MR and CT compatible material. 3D Slicer was required for real-time tracking during treatment.

Results: Based on MR simulation, a treatment plan was created with dose differentials in the area of prior surgery versus normal vaginal tissue. Creation of a low dose CT scan on a mobile CT allowed CT visualization of the applicator for verification. Treatment was administered under the use of a real-time optical tracking with rotational and depth adjustments monitored.

Conclusions: This advanced integration of 3D printed MR and CT biocompatible material, with unique design features consistent with a multi-channel vaginal cylinder, and incorporation of real-time optical tracking ensured that no positional changes were required, allowed successful treatment with differential dosing for a post-operative pediatric vaginal rhabdomyosarcoma patient.

The Prognostic Impact of Preoperative Body Composition in Perihilar and Intrahepatic Cholangiocarcinoma

Publication: Hepatol Commun. 2022 May 26. PMID: 35616275 | PDF

Authors: Lurje I, Czigany Z, Eischet S, Bednarsch J, Ulmer TF, Isfort P, Strnad P, Trautwein C, Tacke F, Neumann UP, Lurje G.

Institution: Department of Hepatology and Gastroenterology, Campus Charité Mitte, Campus Virchow-Klinikum, Charité-Universitätsmedizin Berlin, Berlin, Germany.

Abstract: Cholangiocarcinoma (CCA) is a rare but highly aggressive malignancy of the biliary system. Although it is amenable to surgical resection in early disease, outcomes are frequently dismal. Here, we investigated the prevalence of body composition (BC) alterations and their prognostic role for surgical patients with intrahepatic (iCCA) and perihilar (pCCA) disease. Patients undergoing curative-intent surgery for iCCA or pCCA between 2010 and 2019 at University Hospital Aachen were included. Axial computed tomography images were retrospectively assessed with a segmentation tool, 3D Slicer at the level of the third lumbar vertebra to determine lumbar skeletal muscle (SM) index, mean SM radiation attenuation, and visceral fat area. The related BC pathologies sarcopenia, myosteatosis, visceral obesity, and sarcopenic obesity were determined using previously described cutoffs. A total of 189 patients (86 with iCCA, 103 with pCCA) were included. Alterations of BC were highly prevalent in iCCA and pCCA, respectively: sarcopenia, 33% (28/86) and 39% (40/103); myosteatosis, 66% (57/86) and 66% (68/103); visceral obesity, 56% (48/86) and 67% (69/103); sarcopenic obesity, 11% (9/86) and 17% (17/103). Sarcopenia and myosteatosis did not have a significant prognostic role for disease-free survival (DFS) and overall survival (OS). Patients with iCCA with sarcopenic obesity (n = 9) had significantly shorter OS than patients without sarcopenic obesity (n = 7; log-rank p = 0.002; median OS, 11 months and 31 months; 1-year mortality, 55.6% [5/9] and 22% [17/77]; 5-year mortality, 88.9% [8/9] and 61% [47/77], respectively). In multivariable analysis, only tumor-related risk factors remained prognostic for DFS and OS. Sarcopenic obesity may affect clinical outcomes after curative-intent surgery for iCCA, indicating that imaging-based analysis of BC may hold prognostic value for long-term survival and could aid preoperative patient selection.

HEARTBEAT4D: An Open-source Toolbox for Turning 4D Cardiac CT into VR/AR

Publication: J Digit Imaging. 2022 May 25. PMID: 35614275.

Authors: Bindschadler M, Buddhe S, Ferguson MR, Jones T, Friedman SD, Otto RK.

Institution: Department of Pediatrics, Seattle Children's Heart Center and the University of Washington, Seattle, WA, USA.

Abstract: Four-dimensional data sets are increasingly common in MRI and CT. While clinical visualization often focuses on individual temporal phases capturing the tissue(s) of interest, it may be possible to gain additional insight through exploring animated 3D reconstructions of physiological motion made possible by augmented or virtual reality representations of 4D patient imaging. Cardiac CT acquisitions can provide sufficient spatial resolution and temporal data to support advanced visualization, however, there are no open-source tools readily available to facilitate the transformation from raw medical images to dynamic and interactive augmented or virtual reality representations. To address this gap, we developed a workflow using free and open-source tools to process 4D cardiac CT imaging starting from raw DICOM data and ending with dynamic AR representations viewable on a phone, tablet, or computer. In addition to assembling the workflow using existing platforms (3D Slicer and Unity), we also contribute two new features: 1. custom software which can propagate a segmentation created for one cardiac phase to all others and export to surface files in a fully automated fashion, and 2. a user interface and linked code for the animation and interactive review of the surfaces in augmented reality. Validation of the surface-based areas demonstrated excellent correlation with radiologists' image-based areas (R > 0.99). While our tools were developed specifically for 4D cardiac CT, the open framework will allow it to serve as a blueprint for similar applications applied to 4D imaging of other tissues and using other modalities. We anticipate this and related workflows will be useful both clinically and for educational purposes.

Three-Dimensional Evaluation of Maxillary Second Molar Position in Untreated Patients With Normal Occlusion: Implications for Preadjusted Appliance Prescriptions

Publication: J Orofac Orthop. 2021 Mar 30. PMID: 33783560

Authors: Goracci C, Ruellas AC, Nieri M, Crouch S, McNamara JA Jr, Franchi L.

Institution: Department of Medical Biotechnologies, University of Siena, Policlinico Le Scotte, Siena, Italy.

Abstract: A sample of 41 subjects (16 females, 25 males) was selected from the University of Michigan Growth Study (UMGS). Digital dental casts with fully erupted second molars in occlusion were chosen (mean age 14.9 ± 1.3 years). Digital measurements were recorded with the open source software 3D Slicer. The digital measurements of the UMGS sample were compared with the manual measurements collected by Andrews from his sample of untreated class I subjects with normal overbite and overjet. Two mixed effect models (sagittal and transversal inclinations) were performed. The "random effect" was represented by the subjects, while the "fixed effects" were the two compared groups, the side of the arch (right and left), and the group × side interaction. Outcome variables were sagittal and transversal inclinations of the upper second molars.

Investigating Metacarpi of Hamdani Sheep via Different Measurement and Modelling Methods: A Methodological Study

Publication: Anat Histol Embryol. 2022 May 24. PMID: 35608253.

Authors: Güzel BC, Koçyiğit A, Demircioğlu İ, Demiraslan Y.

Institution: Department of Anatomy, Faculty of Veterinary Medicine, Fırat University, Elazig, Turkey.

Abstract: The aim of the study was to perform the morphometric analyses on metacarpi of Hamdani sheep via different measurement methods and to compare the methods. Thus, metacarpal bones of 15 females and 15 males were used in the study. Measurements were taken from the measurement points determined on metacarpus via four methods, and their statistical analyses were performed. When both male and female metacarpal bones were examined in the De parameter in the comparison with the methods, it was observed that the four measurement methods were different from one another (p < 0.01). When DEM and DEL measurement parameters were examined in male metacarpus, the highest value was measured in ImageJ and the smallest value was measured in 3D Slicer software; however, it was found that the statistical difference was not significant when compared numerically (p > 0.05). As a result, while it was observed that the measurements made by using digital calliper measurements, photometric analysis, and 3D software were similar in some of the parameters but there was no statistically significant difference; whereas, Statistical difference was detected in some parameters.

Smartphone Navigated Endoscopic Port Surgery of Hypertensive Basal Ganglia Hemorrhage

Publication: J Clin Neurosci. 2022 May 21;101:193-197. PMID: 35609413.

Authors: Li F, Gan Z, Xu X, Zhao Y, Wang Q, Chen C, Liu H, Xiong R, Qi Z, Sun G, Zhang J, Xu B, Chen X.

Institution: Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China; Department of Neurosurgery, Hainan Hospital of PLA General Hospital, Sanya, China.

Abstract: Objective: Endoscopic port surgery is a promising alternative for the surgical treatment of intracerebral hypertensive basal ganglia hemorrhage (HBGH). The precise location of hematoma is a crucial step for surgery. The authors developed a simple, low-cost navigation method using an Android smartphone for the localization of HBGH.

Methods: All patients' CT DICOM data were processed with an open-source software, 3D Slicer. The volume of hematoma, angle, and length of trajectory were calculated automatically. A smartphone running the Android system and the Compass APP was used to help insert the inner introducer. An endoscopic port system was applied to create a working channel for neuro-endoscopic hematoma evacuation.

Results: There were 27 patients enrolled in this study (mean age 56). All patients underwent successful surgical evacuation of HBGH with neuroendoscopic evacuation. The mean time taken for the surgical plan was 4 min. The total operation time from skin incision to final suture was 82.6 min. Compared with standard neuronavigation, mean error of trajectory was 5.1 mm. The mean preoperative hematoma volume was 44.8 ml. The optimal trajectory angle averaged 39.5°and the length was 71 mm. Intraoperative blood loss was about 45 ml. Post-operative hematoma volume was 2.9 ml, and the average evacuation rate was 93.6%. One week after surgery, the mean GCS score was improved from 8.2 to 13.8 (p < 0.01).

Conclusions: This simple, low-cost navigation method using 3D Slicer, an Android smartphone with the Compass APP, helps precisely insert the endoscopic working channel to the desired point, which is crucial for satisfactory evacuation of HBGH.

Evidence of Linear Bone Flap Resorption in Patients Undergoing Autologous Cranioplasty Following Decompressive Craniectomy: A 3D Slicer Segmented Analysis of Serial CT Images

Publication: World Neurosurg. 2022 May 18:S1878-8750(22)00677-5. PMID: 35597539.

Authors: Spake CS, Goli R, Beqiri D, Crozier JW, Cielo DJ, Klinge PM, Svokos K, Woo AS.

Institution: Division of Plastic Surgery, The Warren Alpert Medical School of Brown University, Providence, RI, USA.

Abstract: Objectives: Autologous cranioplasty (CP) following decompressive craniectomy (DC) carries risk of bone flap resorption (BFR). The current literature offers limited information regarding the natural progression of BFR, and the rate at which it occurs. We aim to characterize the progression of BFR over time and elucidate risk factors for accelerated BFR.

Methods: A retrospective analysis was conducted on patients who underwent DC and autologous CP. Serial computed tomography (CT) images were used to quantify degree of BFR over time. Risk factors included age, diabetes, smoking status, flap fragmentation, defect size, and DC-CP time interval. Chi-square analyses and Student's t-tests were performed to examine differences between patients who experienced BFR and those who did not.

Results: Overall, 82% of patients demonstrated evidence of clinically relevant resorption on CT. On average, the bone flap decreased in volume by 36.7% within the first year, with a linear loss in volume after multiple years of follow-up. Individuals who developed greater BFR were significantly younger (43 ± 17 vs. 56 ± 12, p=0.022), had a lower incidence of diabetes (5.9% vs. 43%, p=0.037), and had more bone flap fragments (1.4 ± 0.67 vs. 1.00 ± 0, p <0.001) than those who did not.

Conclusion: Resorption following CP with cryopreserved bone appears to progress in a fairly linear and continuous fashion over time. Using serial CT images, we found a resorption rate of 82% at our institution. We identified several possible risk factors for resorption, including flap fragmentation, younger age, and absence of diabetes.

Custom Massive Allograft in a Case of Pelvic Bone Tumour: Simulation of Processing with Computerised Numerical Control vs. Robotic Machining

Publication: J Clin Med. 2022 May 15;11(10):2781. PMID: 35628908 | PDF

Authors: Vivarelli L, Govoni M, Attala D, Zoccali C, Biagini R, Dallari D.

Institution: Reconstructive Orthopaedic Surgery and Innovative Techniques-Musculoskeletal Tissue Bank, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.

Abstract: The use of massive bone allografts after the resection of bone tumours is still a challenging process. However, to overcome some issues related to the processing procedures and guarantee the best three-dimensional matching between donor and recipient, some tissue banks have developed a virtual tissue database based on the scanning of the available allografts for using their 3D shape during virtual surgical planning (VSP) procedures. To promote the use of future VSP bone-shaping protocols useful for machining applications within a cleanroom environment, in our work, we simulate a massive bone allograft machining with two different machines: a four-axes (computer numerical control, CNC) vs. a five-axes (robot) milling machine. The allograft design was based on a real case of allograft reconstruction after pelvic tumour resection and obtained with 3D Slicer and Rhinoceros software. Machining simulations were performed with RhinoCAM and graphically and mathematically analysed with CloudCompare and R, respectively. In this case, the geometrical differences of the allograft design are not clinically relevant; however, the mathematical analysis showed that the robot performed better than the four-axes machine. The proof-of-concept presented here paves the way towards massive bone allograft cleanroom machining. Nevertheless, further studies, such as the simulation of different types of allografts and real machining on massive bone allografts, are needed.

Combination of Preoperative Multimodal Image Fusion and Intraoperative Dyna CT in Percutaneous Balloon Compression of Trigeminal Ganglion for Primary Trigeminal Neuralgia: Experience in 24 Patients

Publication: Front Surg. 2022 May 9;9:895394. PMID: 35615652 | PDF

Authors: Liao CC, Li JY, Wu KH, Jian ZH, Yi XF, Weng ZJ, Chen G.

Institution: Department of Neurosurgery, Zhuhai People's Hospital (Zhuhai Hospital Affifiliated With Jinan University, China), Zhuhai, China.

Abstract: Objective: We retrospectively assessed the surgical results of PBC with preoperative multimodal image fusion and intraoperative Dyna Computed Tomography (CT) in 24 patients with primary trigeminal neuralgia (PTN) to explore a valuable aid for Percutaneous balloon compression (PBC).

Methods: We studied the data of 24 patients with PTN. All patients underwent PBC and were assessed with preoperative multimodal image fusion [computed tomography (CT) and magnetic resonance imaging (MRI)] and intraoperative Dyna CT in the Department of Neurosurgery of Zhuhai People's Hospital between October 2020 and September 2021. Multimodal image fusion-three-dimensional (3D) reconstruction of CT and MRI data-was performed using 3D Slicer software, and preoperative evaluation was performed according to the results of image fusion. Dyna CT was used to dynamically observe the position and shape of the metallic hollow introducer and Fogarty catheter and balloon during the operation to guide the operation in real time. We performed follow-up assessments each month and summarized the clinical characteristics, surgical effects, and complications in all patients.

Results: Surgery was successful for all patients; the patients reported immediate pain relief. Surgical complications included facial numbness in 24 patients (100%), mild masseter weakness in three (12.5%), herpes zoster in three (12.5%), and balloon rupture in one (4.2%). None of the patients had serious surgical complications. The mean follow-up time was 9.6 ± 2.7 months. During the follow-up period, 22 patients (91.7%) experienced no recurrence of pain, and two patients (8.3%) experienced recurrence of pain, of which one underwent secondary PBC surgery.

Conclusions: Preoperative multimodal image reconstruction can help fully evaluate PBC surgery, clarify the etiology, and predict the volume of contrast medium required during the operation. It provided important assistance for PBC treatment of trigeminal neuralgia patients when preoperative multimodal image fusion is combined with intraoperative Dyna CT.

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

Publication: Acad Radiol. 2022 May 13:S1076-6332(22)00253-7. PMID: 35577699.

Authors: Shang H, Li J, Jiao T, Fang C, Li K, Yin D, Zeng Q.

Institution: Department of Radiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, No. 16766 Jingshi Road, Jinan, Shandong, China.

Abstract: Rationale and objectives: To explore the feasibility of differentiating three predominant metastatic tumor types using lung computed tomography (CT) radiomics features based on supervised machine learning.

Materials and methods: This retrospective analysis included 252 lung metastases (LM) (from 78 patients), which were divided into the training (n = 176) and test (n = 76) cohort randomly. The metastases originated from colorectal cancer (n = 97), breast cancer (n = 87), and renal carcinoma (n = 68). An additional 77 LM (from 35 patients) were used for external validation. All radiomics features were extracted from lung CT using an open-source software, 3D Slicer3D Slicer. The least absolute shrinkage and selection operator (LASSO) method selected the optimal radiomics features to build the model. Random forest and support vector machine (SVM) were selected to build three-class and two-class models. The performance of the classification model was evaluated with the area under the receiver operating characteristic curve (AUC) by two strategies: one-versus-rest and one-versus-one.

Results: Eight hundred and fifty-one quantitative radiomics features were extracted from lung CT. By LASSO, 23 optimal features were extracted in three-class, and 25, 29, and 35 features in two-class for differentiating every two of three LM (colorectal cancer vs. renal carcinoma, colorectal cancer vs. breast cancer, and breast cancer vs. renal carcinoma, respectively). The AUCs of the three-class model were 0.83 for colorectal cancer, 0.79 for breast cancer, and 0.91 for renal carcinoma in the test cohort. In the external validation cohort, the AUCs were 0.77, 0.83, and 0.81, respectively. Swarmplot shows the distribution of radiomics features among three different LM types. In the two-class model, high accuracy and AUC were obtained by SVM. The AUC of discriminating colorectal cancer LM from renal carcinoma LM was 0.84, and breast cancer LM from colorectal cancer LM and renal carcinoma LM were 0.80 and 0.94, respectively. The AUCs were 0.77, 0.78, and 0.84 in the external validation cohort.

Conclusion: Quantitative radiomics features based on Lung CT exhibited good discriminative performance in LM of primary colorectal cancer, breast cancer, and renal carcinoma.

Hematoma Segmentation of Spontaneous Intracerebral Hemorrhage Based on Watershed and Region-Growing Algorithm

Publication: Sichuan Da Xue Xue Bao Yi Xue Ban. 2022 May;53(3):511-516. PMID: 35642163

Authors: Zhao JY, Zhou ZS, Wang XY, Zhang HY, Duan ZH, Wang SM, Wan HL, Zhang T.

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

Abstract: Objective: To establish a brain hematoma CT image segmentation method based on watershed and region-growing algorithm so as to measure hematoma volume quickly and accurately, to explore the consistency between the results of this segmentation method and those of manual segmentation, the clinical gold standard, and to compare the results of this method with the calculation of the two Tada formulas commonly used in clinical practice.

Methods: The preoperative CT images of 152 patients who were treated for spontaneous cerebral hemorrhage at the Department of Neurosurgery, West China Hospital, Sichuan University between January 2018 and June 2019 were retrospectively collected. The CT images were randomly assigned, by using a random number table, to the training set, the test set and the validation set, which contained 100 patients, 22 patients and 30 patients, respectively. The labeling results of the training set and the test set were used in algorithm training and testing. Four methods, namely, manual segmentation, algorithm segmentation, i.e., segmentation calculation based on watershed and regional growth algorithm, Tada formula, i.e., the traditional Tada formula calculation, and accurate Tada formula, i.e., accurate Tada formula calculation based on 3D Slicer, were applied on the validation set to measure the hematoma volume. The Digital Imaging and Communications in Medicine (DICOM) data of subjects meeting the selection criteria of the study were manually segmented by two experienced neurosurgeons. The hematoma segmentation model was built based on watershed algorithm and regional growth algorithm. Seed point selected by neurosurgeons was taken as the starting point of growth. Regional grayscale difference criterion combined with manual segmentation validation were adopted to determine the regional growth threshold that met the segmentation precision requirements for intracranial hematoma. Using manual segmentation as the gold standard, Bland-Altman consistency analysis was used to verify the consistency of the three other methods for measuring hematoma volume.

Results: With manual segmentation as the gold standard, among the three methods of measuring hematoma volume, algorithm segmentation had the smallest percentage error, the narrowest range of difference, the highest intra-group correlation coefficient (0.987), good consistency, and the narrowest 95% limits of agreement ( LoA). The percentage error of its segmentation was not statistically significant for hematomas of different volumes.

Conclusion: The segmentation method of spontaneous intracerebral hemorrhage based on watershed and regional growth algorithm shows stable measurement performance and good consistency with the clinical gold standard, which has considerable clinical significance, but it still needs further validation with more clinical samples.

Virtual Planning and Rapid 3D Prototyping Surgical Guide for Anterior Crown Lengthening Surgery: A Clinical Case Report

Publication: J Prosthodont. 2022 Apr;31(4):275-281. PMID: 34932246

Authors: Kim J, Lin YC, Danielak M, Van M, Lee DH, Kim H, Arany PR.

Institution: Department of Oral Biology, School of Dental Medicine, University at Buffalo, NY, USA.

Abstract: Progress with additive 3D printing is revolutionizing biomaterial manufacturing, including clinical dentistry and prosthodontics. Among the several 3D additive printing technologies, stereolithography is very popular as it utilizes light-activated resin for precise resolution. A simplified digital technique was used to fabricate two designs of a surgical guide for crown lengthening. Two cases are presented that utilized digital DICOM files obtained with computed tomography (CT) imaging and processed using four CAD software (Blue Sky Plan, Exocad, Meshmixer and 3D Slicer). The final models were converted to standard tesselation (STL) files and the guides were 3D printed with an additive sterelithography (SLA) printer. The first case was fabricated with a bone model from CBCT data, and the second case was generated with intraoral and wax-up scans alone. Both methods appear to be equally effective compared to using a conventional method of guide frabication. However, proximal bone reduction was a concern with both designs. Digitally fabricated 3D printed surgical guide for crown lengthening has merit and a practical design is needed for future clinical validation. This article is protected by copyright. All rights reserved.

A New Simple, Cost-Effective Navigation System (EASY Navigator) for Neurosurgical Interventions

Publication: World Neurosurg. 2022 Apr 29;164:143-7. PMID: 35490891.

Authors: Faraj MK, Kailan SL, Al-Neami AQH.

Institution: Department of Surgery, Consultant Neurosurgeon, College of Medicine, University of Baghdad, Baghdad, Iraq.

Abstract: Navigation technique facilitates reaching deeply seated masses more precisely with the least sacrifice of normal tissues. There are 2 primary navigation systems: electromagnetic and infrared (optical). The technique is based on recording the head position intraoperatively and merging this image with preoperative magnetic resonance imaging.

Methods: We tried to replace these conventional navigating systems with a simple technique using free software, 3D Slicer and a computer air mouse. The study was designed into 3 stages. In stage 1, we used this method on 3-dimensional printed models of patients' magnetic resonance images with deeply seated brain tumors. In stage 2, we performed the surgeries on patients. In the last stage, we used both the conventional navigation system with our method simultaneously on the same patients and compared the accuracy of both methods.

Results: This new system was as accurate as conventional navigating systems, ranging from ±2 mm.

Conclusions: This new technique, if done properly, can replace conventional methods with less time of preparation, and its cost is almost free.

3D Visualization of Perianal Fistulas Using Parametric Models

Publication: Tech Coloproctol. 2022 Apr;26(4):291-300. PMID: 35094202

Authors: Navkar NV, Balakrishnan S, Kharbech S, Sabawi M, Abinahed J, Ahmed A, Al-Ansari A, Omar A, Khanna M, Darweesh A.

Institution: Department of Surgery, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar.

Abstract: Background: Magnetic resonance imaging (MRI) is used as a standard for assessment of complex perianal fistulas. Apart from textual description of the case, 3D reconstructed models from MRI further aid in understanding the entire anatomy of the fistula tract and its relation to the pelvic floor. This information is crucial as it helps surgeons to understand the extent and complexity of the disease before surgical treatment. However, 3D model generation from MRI is a time-consuming step for a radiologist as it requires tedious manual delineations to be performed on every slice of the images. The aim of this study was to develop a method that could enable radiologists to present enhanced information to surgeons for treatment of complex perianal fistulas while simultaneously reducing the manual efforts and time required to generate the information.

Methods: A method was proposed to depict relevant anatomies of complex perianal fistula as parametric models in three-dimensional (3D) space. A plugin inside 3D Slicer software was developed for the generation of the parametric models from MRI. The levator ani muscle, internal sphincter, and external sphincter are represented as tubular structures, whereas fistula tracks and abscess are presented as splines.

Results: Parametric models were generated to depict three cases of complex perianal fistulas and similarity measures were computed for ten cases. Visual comparison of the parametric models was made with the 3D models generated by the standard approach. The parametric models took less time to create and were able to visually present enriched information as compared to the 3D models generated by the standard approach.

Conclusions: The proposed method, using parametric models, shows potential for faster generation and better visualization of the 3D information required for the treatment of complex perianal fistula cases.

Optimized Tractography Mapping and Quantitative Evaluation of Pyramidal Tracts for Surgical Resection of Insular Gliomas: a Correlative Study with Diffusion Tensor Imaging-Derived Metrics and Patient Motor Strength

Publication: J Digit Imaging. 2022 Apr;35(2):356-64. PMID: 35064370

Authors: Li Y, Hou Y, Li Q, Tang J, Lu J.

Institution: Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.

Abstract: We investigate the correlation between diffusion tensor imaging (DTI)-derived metric statistics and motor strength grade of insular glioma patients after optimizing the pyramidal tract (PT) delineation. Motor strength grades of 45 insular glioma patients were assessed. All the patients underwent structural and diffusion MRI examination before and after surgery. We co-registered pre- and post-op datasets, and a two-tensor unscented Kalman filter (UKF) algorithm was employed to delineate bilateral PTs after DWI pre-processing. The tractography results were voxelized, and their labelmaps were cropped according to the location of frontal and insular parts of the lesion. Both the whole and cropped labelmaps were used as regions of interest to analyze fractional anisotropy (FA) and Trace statistics; hence, their ratios were calculated (lesional side tract/contralateral normal tract). The combination of DWI pre-processing and two-tensor UKF algorithm successfully delineated bilateral PTs of all the patients. It effectively accomplished both full fiber delineation within the edema and an extensive lateral fanning that had a favorable correspondence to the bilateral motor cortices. Before surgery, correlations were found between patients' motor strength grades and ratios of PT volume and FA standard deviation (SD). Nearly 3 months after surgery, correlations were found between motor strength grades and the ratios of metric statistics as follows: whole PT volume, whole mean FA, and FA SD. We substantiated the correlation between DTI-derived metric statistics and motor strength grades of insular glioma patients. Moreover, we posed a workflow for comprehensive pre- and post-op DTI quantitative research of glioma patients.

Keywords: 3D Slicer; Diffusion tensor imaging; Insular glioma; Pyramidal tracts.

The Significance of Nanoparticles in Brain Cancer Diagnosis and Treatment: Modeling and Simulation

Publication: Biomed Phys Eng Express. 2022 Apr 22;8(3). PMID: 35405668.

Authors: Badawi MI, Hafez KS.

Institution: Biomedical Equipment Technology Department, Faculty of Applied Health Sciences Technology, Pharos University, Alexandria, Egypt.

Abstract: A numerical analysis of specific absorption rate (SAR) and temperature distributions in a realistic human head model is presented in this study. The key challenge is to rise cancer temperature to an optimal temperature without heating nearby healthy tissues. The model's uniqueness is that it captures the effect of nanoparticles on both brain cancer diagnosis and treatment. A realistic human head model with a cancerous brain segmented from 2D magnetic resonance imaging (MRI) gained from an actual patient using 3D Slicer, modeled, and simulated using CST-Microwave Studio, and illuminated by Archimedes spiral antenna. At frequencies of 2450 MHz and 915 MHz, the model simulated the absence and presence of various nanoparticles. The obtained results suggest that when using nanoparticles, it is possible to achieve sufficient energy deposition and temperature rise to therapeutic values (greater than 42 °C) in brain cancers using the proposed noninvasive hyperthermia system at 915 MHz frequency, especially for gold nanoparticles, without harming surrounding healthy tissue. Our research might pave the way for a clinical applicator prototype that can heat brain cancer.

Three-Dimensional Assessment of Tongue Cancer Prognosis by Preoperative MRI

Publication: Oral Dis. 2022 Apr 15. PMID: 35426211.

Authors: Li C, Zhu L, Guo Y, Ji T, Ren Z.

Institution: Department of Oral and Maxillofacial Head and Neck Oncology, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Abstract: Purpose: To obtain the relative volume by measuring the tongue volume and the lesion volume, and further explore its relationship with the prognosis of patients, hoping to supplement the TNM staging with a new index.

Methods: ITK-SANP software was used to outline the patients' MRI. After MRI reconstruction and measurement, 3D Slicer software was used to estimate tumor volume.

Results: A total of 64 patients with tongue cancer who met the inclusion criteria were included in the study. The estimated tumor volume after MRI reconstruction revealed a significant and robust correlation with tumor stage (p < 0.05, Rs = 0.6207) and a substantial and medium correlation with early lymph node metastasis (p < 0.05, Rs = 0.4873).

Conclusions: We classified tongue cancer into three grades based on tumor volume (Stage I, tumors smaller than 1500 mm³; Stage II, tumors 1500-9000 mm³; and Stage III, tumors larger than 9000 mm³), and such grading could be used as a reference for tumor staging, lymph node metastasis, and patient prognosis to a certain extent.

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

Publication: Oral Maxillofac Surg. 2022 Apr 15. PMID: 35426586.

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

Institution: Department of Oral and Maxillofacial Surgery, Federal University of Ceará Campus Sobral, Sobral, Ceará, Brazil.

Abstract: Purpose: This study aimed to analyze alterations in mandibular positioning after surgically assisted maxillary expansion (SARME) with and without pterygoid disjunction (PD).

Methods: Cone-beam computed tomography scans of 24 healthy individuals (18-45 years old) with transverse deficiency, superior to 5 mm, underwent SARME with or without PD. The aspects prospectively assessed were (1) alignment and position of the head (ITK-Snap and 3D Slicer software); (2) McNamara's and Steiner-Tweed-Wits' cephalometric analysis (Dolphin Imaging®); and (3) colorimetric evaluation based on 3D correspondence analysis (3D Slicer software).

Results: A decrease in 1-NA and 1-SN angles as well as an increased occlusal plane in both groups was observed. Superior-inferior and anteroposterior spatial displacements of the chin were statistically significant in the PD group. Altered colorimetric patterns were also observed in the PD group.

Conclusions: This study found more evident tooth inclination in the group without PD; mandibular alterations were more evident in the PD group. Further studies with 3D analysis are strongly recommended for more comprehensive results.

Reproducibility for Hepatocellular Carcinoma CT Radiomic Features: Influence of Delineation Variability Based on 3D-CT, 4D-CT and Multiple-Parameter MR Images

Publication: Front Oncol. 2022 Apr 14;12:881931. PMID: 35494061. PDF

Authors: Duan J, Qiu Q, Zhu J, Shang D, Dou X, Sun T, Yin Y, Meng X.

Institution: School of Precision Instrument and Opto-electronics Engineering, Tianjin University, Tianjin, China.

Abstract: Purpose: Accurate lesion segmentation is a prerequisite for radiomic feature extraction. It helps to reduce the features variability so as to improve the reporting quality of radiomics study. In this research, we aimed to conduct a radiomic feature reproducibility test of inter-/intra-observer delineation variability in hepatocellular carcinoma using 3D-CT images, 4D-CT images and multiple-parameter MR images.

Materials and methods: For this retrospective study, 19 HCC patients undergoing 3D-CT, 4D-CT and multiple-parameter MR scans were included in this study. The gross tumor volume (GTV) was independently delineated twice by two observers based on contrast-enhanced computed tomography (CECT), maximum intensity projection (MIP), LAVA-Flex, T2W FRFSE and DWI-EPI images. We also delineated the peritumoral region, which was defined as 0 to 5 mm radius surrounding the GTV. 107 radiomic features were automatically extracted from CECT images using 3D Slicer software. Quartile coefficient of dispersion (QCD) and intraclass correlation coefficient (ICC) were applied to assess the variability of each radiomic feature. QCD<10% and ICC≥0.75 were considered small variations and excellent reliability. Finally, the principal component analysis (PCA) was used to test the feasibility of dimensionality reduction.

Results: For tumor tissues, the numbers of radiomic features with QCD<10% indicated no obvious inter-/intra-observer differences or discrepancies in 3D-CT, 4D-CT and multiple-parameter MR delineation. However, the number of radiomic features (mean 89) with ICC≥0.75 was the highest in the multiple-parameter MR group, followed by the 3DCT group (mean 77) and the MIP group (mean 73). The peritumor tissues also showed similar results. A total of 15 and 7 radiomic features presented excellent reproducibility and small variation in tumor and peritumoral tissues, respectively. Two robust features showed excellent reproducibility and small variation in tumor and peritumoral tissues. In addition, the values of the two features both represented statistically significant differences among tumor and peritumoral tissues (P<0.05). The PCA results indicated that the first seven principal components could preserve at least 90% of the variance of the original set of features.

Conclusion: Delineation on multiple-parameter MR images could help to improve the reproducibility of the HCC CT radiomic features and weaken the inter-/intra-observer influence.

Pseudoprogression Prediction in High Grade Primary CNS Tumors by Use of Radiomics

Publication: Sci Rep. 2022 Apr 8;12(1):5915. PMID: 35396525. | PDF

Authors: Ari AP, Akkurt BH, Musigmann M, Mammadov O, Blömer DA, Kasap DNG, Henssen DJHA, Nacul NG, Sartoretti E, Sartoretti T, Backhaus P, Thomas C, Stummer W, Heindel W, Mannil M.

Institution: University Clinic for Radiology, Westfälische Wilhelms-University Muenster and University Hospital Muenster, Albert-Schweitzer-Campus 1, Muenster, Germany.

Abstract: Our aim is to define the capabilities of radiomics and machine learning in predicting pseudoprogression development from pre-treatment MR images in a patient cohort diagnosed with high grade gliomas. In this retrospective analysis, we analysed 131 patients with high grade gliomas. Segmentation of the contrast enhancing parts of the tumor before administration of radio-chemotherapy was semi-automatically performed using the 3D Slicer open-source software platform (version 4.10) on T1 post contrast MR images. Imaging data was split into training data, test data and an independent validation sample at random. We extracted a total of 107 radiomic features by hand-delineated regions of interest (ROI). Feature selection and model construction were performed using Generalized Boosted Regression Models (GBM). 131 patients were included, of which 64 patients had a histopathologically proven progressive disease and 67 were diagnosed with mixed or pure pseudoprogression after initial treatment. Our Radiomics approach is able to predict the occurrence of pseudoprogression with an AUC, mean sensitivity, mean specificity and mean accuracy of 91.49% [86.27%, 95.89%], 79.92% [73.08%, 87.55%], 88.61% [85.19%, 94.44%] and 84.35% [80.19%, 90.57%] in the full development group, 78.51% [75.27%, 82.46%], 66.26% [57.95%, 73.02%], 78.31% [70.48%, 84.19%] and 72.40% [68.06%, 76.85%] in the testing group and finally 72.87% [70.18%, 76.28%], 71.75% [62.29%, 75.00%], 80.00% [69.23%, 84.62%] and 76.04% [69.90%, 80.00%] in the independent validation sample, respectively. Our results indicate that radiomics is a promising tool to predict pseudo-progression, thus potentially allowing to reduce the use of biopsies and invasive histopathology.

Radiomics Analysis Based on Lumbar Spine CT to Detect Osteoporosis

Publication: Eur Radiol. 2022 Apr 30:1-8. PMID: 35499565. | PDF

Authors: Jiang YW, Xu XJ, Wang R, Chen CM.

Institution: Department of Neurosurgery, Fujian Medical University Union Hospital, No. 29, Xin Quan Road, Fuzhou City, Fujian Province, China.

Abstract: Objectives: Undiagnosed osteoporosis may lead to severe complications after spinal surgery. This study aimed to construct and validate a radiomic signature based on CT scans to screen for lumbar spine osteoporosis.

Methods: Using a stratified random sample method, 386 vertebral bodies were randomly divided into a training set (n = 270) and a test set (n = 116). A total of 1040 radiomics features were automatically retracted from lumbar spine CT scans using the 3D Slicer pyradiomics module, and a radiomic signature was created. The sensitivity, specificity, accuracy, and area under the receiver operating characteristic curve (AUC) of the Hounsfield and radiomics signature models were calculated. The AUCs of the two models were compared using the DeLong test. Their clinical usefulness was assessed using a decision curve analysis.

Results: Twelve features were chosen to establish the radiomic signature. The AUCs of the radiomics signature and Hounsfield models were 0.96 and 0.88 in the training set and 0.92 and 0.84 in the test set, respectively. According to the DeLong test, the AUCs of the two models were significantly different (p < 0.05). The radiomics signature model indicated a higher overall net benefit than the Hounsfield model, as determined by decision curve analysis.

Conclusions: The CT-based radiomic signature can differentiate patients with/without osteoporosis prior to lumbar spinal surgery. Without additional medical cost and radiation exposure, the radiomics method may provide valuable information facilitating surgical decision-making.

Key points: • The goal of the study was to evaluate the efficacy of a radiomics signature model based on routine preoperative lumbar spine CT scans in screening osteoporosis. • The radiomics signature model demonstrated excellent prediction performance in both the training and test sets. • This radiomics method may provide valuable information and facilitate surgical decision-making without additional medical costs and radiation exposure.

Giant Pediatric Supratentorial Tumor: Clinical Feature and Surgical Strategy

Publication: Front Pediatr. 2022 Apr 26;10:870951. PMID: 35558365. | PDF

Authors: Zhang ZD, Fang HY, Pang C, Yang Y, Li SZ, Zhou LL, Bai GH, Sheng HS.

Institution: Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.

Abstract: To analyze the clinical character of giant pediatric supratentorial tumor (GPST) and explore prognostic factors.

Materials and methods: We analyzed the clinical data comprising of 35 cases of GPST from a single center between January 2015 and December 2020. The tumor volume was measured by 3D Slicer software based on preoperative magnetic resonance imaging (MRI). Glasgow Outcome Scale (GOS) was used to evaluate the short-term prognosis.

Result: The tumor volume varied from 27.3 to 632.8 ml (mean volume 129.8 ml/ median volume 82.8 ml). Postoperative histopathological types include ependymoma, pilocytic astrocytoma, choroid plexus papilloma (CPP), craniopharyngioma, primitive neuroectoderm tumor (PNET), choroid plexus carcinoma (CPC), immature teratoma, atypical teratoid rhabdoid tumor (AT/RT), anaplastic astrocytoma, and gangliocytoma. Tumors in children younger than 3 years and tumors located at the hemispheres appeared to be larger than their respective counterparts, though no statistical significance was found. A patient with giant immature teratoma died during the operation because of excessive bleeding. Postoperative complications include cerebrospinal fluid subgaleal collection/effusion, infection, neurological deficits, and seizures. The mean GOS score of patients with GPST in 6 months is 3.43 ± 1.12, and 83% of patients (29/35) showed improvement. Favorable GPST characteristics to indicated better GOS included small tumor (≤100 ml) (p = 0.029), low-grade (WHO I-II) (p = 0.001), and gross total resection (GTR) (p = 0.015). WHO grade was highly correlated with GOS score (correlation coefficient = -0.625, p < 0.001). GTR and tumor volume were also correlated (correlation coefficient = -0.428, p = 0.010).

Conclusion: The prognosis of GPST is highly correlated with the histopathological type. Smaller tumors are more likely to achieve GTR and might lead to a higher GOS score. Early diagnosis and GTR of the tumor are important for GPST management.

Volumetric Assessment of Changes in the Alveolar Ridge Dimension Following GBR Using a Combination FDBA With Collagen Membrane or Novel Resorbable Scaffold: A Prospective Two-Center Clinical Trial

Publication: J Periodontol. 2022 Mar;93(3):343-53. PMID: 34245016

Authors: Dowlatshahi S, Chen CY, Zigdon-Giladi H, Horwitz J, Ahn C, Kim DM, Machtei EE.

Institution: Division of Periodontology, Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA.

Abstract: Background: The aim of this study was to examine osseous changes following lateral bone augmentation using a novel Ossix Volumax (OV) scaffold alone and compare it to combination therapy using freeze-dried bone allograft (FDBA) and resorbable collagen membrane (FDBA/CM).

Methods: Thirty patients completed this 9-months prospective two-center cohort clinical trial. Before surgery and 9-months re-entry, linear measurements were performed, and impressions taken. Cone-beam computed tomography (CBCT) were done at baseline and 9 months. DICOM slice data were converted into volumetric images using 3D Slicer. Following 3D volumetric image construction, pre- and post-op Standard Triangle Language files were superimposed and volumetric data were extracted for a 10-mm region of interest. Linear measurements were compared similarly.

Results: Baseline clinical parameters were similar in both groups (4.22 and 4.53 mm for OV and FDBA/CM at -2 mm, respectively). Following treatment, vertical distance from the stent had changed minimally (-0.36 and -0.12 mm, respectively). Similarly, lateral bone gain ranged from 0 to 0.4 mm, for both groups. To the contrary, the CBCT measurements showed a significantly greater increase in horizontal width in the control at -2 mm (0.95 ± 0.2 mm) compared with -0.62 mm for the OV (P = 0.000). Similar changes were observed at -5 mm (0.63 and -0.41 mm, respectively, P = 0.01). Sites volume had increased from 266 ± 149 mm3 to 360 ± 138 mm3 (P = 0.001) for FDBA/CM with negligible changes for OV (from 334 to 335 mm3 , P = 0.952). these between-group changes being statistically significant (P = 0.023).

Conclusion: FDBA/CM yielded better albeit moderate increase in the volume of the edentulous ridge, while OV scaffolds failed to produce similar results.

Choroidal Macrovessel: Systematic Review and Analysis of Anatomic Origin

Publication: Surv Ophthalmol. 2022 Mar-Apr;67(2):570-8. PMID: 34332961

Authors: Bowen RC, Raval V, Soto H, Singh AD.

Institution: Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA.

Abstract: There are various hypotheses for the anatomic origin of a choroidal macrovessel. We assess whether a choroidal macrovessel is a dilated posterior ciliary artery. A systematic review of published literature on choroidal macrovessels was performed with two additional cases from our institution. We compared the visible entry and vascular course of the macrovessel in the published literature. We performed a comparative analysis using indocyanine green angiography, swept source optical computed tomography, and 3D reconstruction of two choroidal macrovessels using 3D Slicer (Harvard, Boston, USA). From the 14 studies found, 18 cases met inclusion criteria. The reported literature and our two cases showed a radiating course along a sectoral distribution pattern of either short or long posterior ciliary arteries. Our review of literature and 3D reconstruction analysis support the hypothesis that choroidal macrovessels are dilated posterior ciliary arteries.

Using Three-Dimensional Visualization as an Optimal Tool to Plan and Validate an Aortopexy in a Congenital Heart Disease Patient With Severe Tracheal Stenosis

Publication: Interact Cardiovasc Thorac Surg. 2022 Mar 31;34(4):708-10. PMID: 34738096

Authors: Kehl T, van Rüth V, Weinrich JM, Hübler M.

Institution: Clinic for Children's Heart Medicine, University Heart & Vascular Center, University Hospital Hamburg-Eppendorf, Hamburg, Germany.

Abstract: We present a patient with severe tracheal stenosis resulting from a compression by the innominate artery 6 months after an arterial switch operation in a dextro-transposition of the great arteries. Segmentation and three-dimensional (3D) visualization were derived from a contrast-enhanced dual-source computed tomography and post-processing was performed using a dedicated open-source platform, 3D Slicer. Post-processing allowed a comprehensible visualization of the relationship of the innominate artery to the trachea when compared to standard computer tomography reformations. Finally, the surgical approach to move the innominate artery anteriorly in order to relieve the tracheal obstruction was emphasized based on the improved 3D visualization of the actual pathology. An effective aortopexy could be performed and the postoperative result was confirmed by a second 3D visualization. About 3 months of follow-up, the patient is completely asymptomatic. Three-dimensional visualization offers excellent opportunities for diagnosis, treatment planning and follow-up in patients with a vascular-related tracheal stenosis in the context of congenital heart disease.

Bladder Urothelial Carcinoma: Machine Learning-based Computed Tomography Radiomics for Prediction of Histological Variant

Publication: Acad Radiol. 2022 Mar 26:S1076-6332(22)00116-7. PMID: 35351362.

Authors: Evrimler S, Ali Gedik M, Ahmet Serel T, Ertunc O, Alperen Ozturk S, Soyupek S.

Institution: Department of Radiology, Suleyman Demirel University School of Medicine, Isparta, 32260, Turkey.

Abstract: Rationale and objectives: Histological variant (HV) of bladder urothelial carcinoma (UC) is a significant factor for therapy management. We aim to assess the predictive performance of machine learning (ML)-based Computed Tomography radiomics of UC for HV.

Materials and methods: Volume of interest of 37 bladder UC tumors, of which 21 were pure and 16 were HV, were manually segmented. The extracted first- and second-order texture features (n = 117) using 3D Slicer radiomics were compared to the radical cystectomy histopathological results. ML algorithms were performed to determine the significant models using Python 2.3, Pycaret library. The sample size was increased to 74 by synthetic data generation, and three outliers from the training set were removed (training dataset; n = 52, test dataset; n = 19). The predictive performances of 15 ML algorithms were compared. Then, the best two models were evaluated on the test set and ensembled by Voting Classifier.

Results: The ML algorithms demonstrated area under curve (AUC) and accuracy ranging 0.79-0.97 and 50%-90%, respectively on the train set. The best models were Gradient Boosting Classifier (AUC: 0.95, accuracy: 90%) and CatBoost Classifier (AUC: 0.97, accuracy: 85%). On the test set; the Voting Classifier of these two models demonstrated AUC, accuracy, recall, precision, and F1 scores as follows; 0.93, 79%, 86%, 67%, and 75%, respectively.

Conclusion: ML-based Computed Tomography radiomics of UC can predict HV, a prognostic factor that is indeterminable by qualitative radiological evaluation and can be missed in the preoperative histopathological specimens.

Semi-Automatic Segmentation of Cone Beam Computed Tomography Datasets for Volume Measurements of Equine Cheek Teeth

Publication: J Vet Dent. 2022 Mar;39(1):41-48. PMID: 34866465

Authors: Herren FL, Gerber V, Meier R, Schweizer-Gorgas D, Klopfenstein Bregger MD.

Institution: University of Bern, Switzerland.

Abstract: The volumes of equine teeth may change considerably over time for several reasons including domestication, routine dental floating, and the hypsodont and anelodont nature of the teeth. Cone beam computed tomography (CBCT) of the head is routinely performed in standing horses and, in this proof of concept study, the feasibility of measuring tooth volume from CBCT datasets was determined. The CBCT images of 5 equine cadaver cheek teeth were segmented with a 3D Slicer software using a predefined protocol, corrected manually, and re-assembled into a 3D model. Individual tooth volume (VS) was calculated from the model. After extraction, the volumes were also measured using the "gold-standard" water displacement method (VW) for comparison. The VS of 77 teeth ranged from 7114 to 42,300 mm3 which strongly correlated with VW (r = 0.99), and on average VS was 6.1% less than VW. There was no significant difference in VS between the right and left arcades in individual animals. Maxillary cheek tooth volume was on average 40% larger than it was for mandibular counterparts. Semi-automatic image segmentation of equine cheek teeth from CBCT data is feasible and accurate but requires some manual intervention. This preliminary study provides initial data on the volume of equine cheek teeth and creates new possibilities for future in vivo studies.

Radiomics-Based Artificial Intelligence Differentiation of Neurodegenerative Diseases with Reference to the Volumetry

Publication: Life (Basel). 2022 Mar 31;12(4):514. PMID: 35455005. | PDF

Authors: Cheung EYW, Chau ACM, Tang FH, On Behalf Of The Alzheimer's Disease Neuroimaging Initiative.

Institution: School of Medical Health and Sciences, Tung Wah College, 19/F, 31 Wylie Road, Ho Man Tin, Hong Kong, China.

Abstract: This study aimed to build automated detection models-one by brain regional volume (V-model), and the other by radiomics features of the whole brain (R-model)-to differentiate mild cognitive impairment (MCI) from cognitive normal (CN), and Alzheimer's Disease (AD) from mild cognitive impairment (MCI). The objectives are to compare the models and identify whether radiomics or volumetry can provide a better prediction for differentiating different types of dementia.

Method: 582 MRI T1-weighted images were retrieved from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, which is a multicenter operating open source database for AD. In total, 97 images of AD, 293 images of MCI patient and 192 images of cognitive normal were divided into a training, a validation and a test group at a ratio of 70:15:15. For each T1-weighted image, volumetric segmentation was performed with the image analysis software FreeSurfer, and radiomics features were retrieved by imaging research software 3D Slicer. Brain regional volume and radiomics features were used to build the V-model and R-model, respectively, using the random forest algorithm by R. The receiver operating characteristics (ROC) curve of both models were used to evaluate their diagnostic accuracy and reliability to differentiate AD, MCI and CN.

Results: To differentiate MCI and CN, both V-model and R-model achieved excellent performance, with an AUC of 0.9992 ± 0.0022 and 0.9850 ± 0.0032, respectively. No significant difference was found between the two AUCs, indicating both models attained similar good performance. In MCI and AD differentiation, the V-model and R-model yielded AUC of 0.9986 ± 0.0013 and 0.9714 ± 0.0175, respectively. The best performance was to differentiate AD from CN, where the V-model and R-model yielded AUC of 0.9994 ± 0.0019 and 0.9830 ± 0.009, respectively. The results suggested that both volumetry and radiomics approaches could be used in differentiating AD, MCI and CN, based on T1 weighted MR images using random forest algorithm successfully.

Conclusion: This study showed that the radiomics features from T1-weighted MR images achieved excellence performance in differentiating AD, MCI and CN. Compared to the volumetry method, the accuracy, sensitivity and specificity are slightly lower in using radiomics, but still attained very good and reliable classification of the three stages of neurodegenerations. In view of the convenience and operator independence in feature extraction, radiomics can be a quantitative biomarker to differentiate the disease groups.

Generating Patient-Matched 3D-Printed Pedicle Screw and Laminectomy Drill Guides From Cone Beam CT Images: Studies in Ovine and Porcine Cadavers

Publication: Med Phys. 2022 Apr 21. PMID: 35445429.

Authors: Kanawati A, Constantinidis A, Williams Z, O'Brien R, Reynolds T.

Institution: Westmead Hospital, Sydney, NSW, Australia.

Abstract: Background: The emergence of robotic Cone Beam Computed Tomography (CBCT) imaging systems in trauma departments has enabled 3D anatomical assessment of musculoskeletal injuries, supplementing conventional 2D fluoroscopic imaging for examination, diagnosis, and treatment planning. To date, the primary focus has been on trauma sites in the extremities.

Purpose: To determine if CBCT images can be used during the treatment planning process in spinal instrumentation and laminectomy procedures, allowing accurate 3D-printed pedicle screw and laminectomy drill guides to be generated for the cervical and thoracic spine.

Methods: The accuracy of drill guides generated from CBCT images was assessed using animal cadavers (ovine and porcine). Preoperative scans were acquired using a robotic CBCT C-arm system, the Siemens ARTIS pheno (Siemens Healthcare, GmbH, Germany). The CBCT images were imported into 3D Slicer v.4.10.2 where vertebral models and specific guides were developed and subsequently 3D-printed. In the ovine cadaver, 11 pedicle screw guides from the T1-T5 and T7-T12 vertebra and six laminectomy guides from the C2-C7 vertebra were planned and printed. In the porcine cadaver, nine pedicle screw guides from the C3-T4 vertebra were planned and printed. For the pedicle screw guides, accuracy was assessed by three observers according to pedicle breach via the Gertzbein-Robbins grading system as well as measured mean axial and sagittal screw error via postoperative CBCT and CT scans. For the laminectomies, the guides were designed to leave 1 mm of lamina. The average thickness of the lamina at the mid-point was used to assess the accuracy of the guides, measured via postoperative CBCT and CT scans from three observers. For all measurements, the intraclass correlation coefficient (ICC) was calculated to determine observer reliability.

Results: Compared with the planned screw angles for both the ovine and porcine procedures (n = 32), the mean axial and sagittal screw error measured on the postoperative CBCT scans from three observers were 3.9 ± 1.9° and 1.8 ± 0.8°, respectively. The ICC among the observes was 0.855 and 0.849 for the axial and sagittal measurements, respectively, indicating good reliability. In the ovine cadaver, directly comparing the measured axial and sagittal screw angle of the visible screws (n = 14) in the postoperative CBCT and conventional CT scans from three observers revealed an average difference 1.9 ± 1.0° in axial angle and 1.8 ± 1.0° in the sagittal angle. The average thickness of the lamina at the middle of each vertebra, as measured on-screen in the postoperative CBCT scans by three observes was 1.6 ± 0.2 mm. The ICC among observers was 0.693, indicating moderate reliability. No lamina breaches were observed in the postoperative images.

Conclusion: Here, CBCT images have been used to generate accurate 3D-printed pedicle screw and laminectomy drill guides for use in the cervical and thoracic spine. The results demonstrate sufficient precision compared with those previously reported, generated from standard preoperative CT and MRI scans, potentially expanding the treatment planning capabilities of robotic CBCT imaging systems in trauma departments and operating rooms.

A Hybrid Registration Method Using the Mandibular Bone Surface for Electromagnetic Navigation in Mandibular Surgery

Publication: Int J Comput Assist Radiol Surg. 2022 Apr 20. PMID: 35441961.

Authors:de Geer AF, van Alphen MJA, Zuur CL, Loeve AJ, van Veen RLP, Karakullukcu MB.

Institution: Verwelius 3D Lab, Department of Head and Neck Surgery and Oncology, Netherlands Cancer Institute, Antoni van Leeuwenhoek, Amsterdam, The Netherlands.

Abstract: Purpose: To utilize navigated mandibular (reconstructive) surgery, accurate registration of the preoperative CT scan with the actual patient in the operating room (OR) is required. In this phantom study, the feasibility of a noninvasive hybrid registration method is assessed. This method consists of a point registration with anatomic landmarks for initialization and a surface registration using the bare mandibular bone surface for optimization.

Methods: Three mandible phantoms with reference notches on two osteotomy planes were 3D printed. An electromagnetic tracking system in combination with 3D Slicer software was used for navigation. Different configurations, i.e., different surface point areas and number and configuration of surface points, were tested with a dentate phantom (A) in a metal-free environment. To simulate the intraoperative environment and different anatomies, the registration procedure was also performed with an OR bed using the dentate phantom and two (partially) edentulous phantoms with atypical anatomy (B and C). The accuracy of the registration was calculated using the notches on the osteotomy planes and was expressed as the target registration error (TRE). TRE values of less than 2.0 mm were considered as clinically acceptable.

Results: In all experiments, the mean TRE was less than 2.0 mm. No differences were found using different surface point areas or number or configurations of surface points. Registration accuracy in the simulated intraoperative setting was-mean (SD)-0.96 (0.22), 0.93 (0.26), and 1.50 (0.28) mm for phantom A, phantom B, and phantom C.

Conclusion: Hybrid registration is a noninvasive method that requires only a small area of the bare mandibular bone surface to obtain high accuracy in phantom setting. Future studies should test this method in clinical setting during actual surgery.

A Predictive Nomogram for Atypical Meningioma Based On Preoperative Magnetic Resonance Imaging and Routine Blood Tests

Publication: World Neurosurg. 2022 Apr 14. PMID: 35430397.

Authors: Lin Y, Dai P, Lin Q, Chen J.

Institution: Dongshan County Hospital of Fujian Province, Zhangzhou, Fujian, China.

Abstract: Objective: The objective of the study was to establish a 5-year progression-free survival prediction nomogram using preoperative routine blood tests and magnetic resonance imaging to guide postoperative treatment.

Methods: Our study was a retrospective analysis of patients with atypical meningioma admitted into our facility from January 31, 2010, to January 31, 2016. We used single-factor logistic analysis to extract valuable indicators from preoperative blood test results and 3D Slicer software to extract radiomic features from magnetic resonance imaging. The radiomics score was calculated by least absolute shrinkage and selection operator logistic regression analysis. We then combined blood indicators and radiomic signatures to construct a radiomic nomogram image. The performance of the model was evaluated comprehensively using the following three aspects: recognition ability, accuracy, and clinical value.

Results: Six significant radiological features were selected through least absolute shrinkage and selection operator logistic regression analysis. The radiometric label established by these six features has satisfactory predictive performance. The area under the curve in the training group was 0.885 (95% confidence interval, 0.8037-0.9659), and the area under the curve in the validation set was 0.789 (95% confidence interval, 0.6092-0.9686). We used the combined image tags and preoperative leukocyte and neutrophil count to construct a 5-year progression-free survival prediction nomogram.

Conclusions: The analysis results of the calibration curve and the decision curve show that the nomogram constructed by combining radiomics and preoperative blood tests has a good predictive value for 5-year progression-free survival in atypical meningioma and can provide a reference for selecting postoperative treatment options.

Optimized Fitting of a Midface Implant to Anchor a Magnetic Nasal Prosthesis Using 3D Printing

Publication: HNO. 2022 Mar;70(3):200-205. PMID: 34463790

Authors: Wrobel C, Keppeler D, Meyer AC.

Institution: Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsmedizin Göttingen, Georg-August-Universität Göttingen, Göttingen, Deutschland.

Abstract: Background: Plate-based anchorage systems for craniofacial prostheses offer advantages over extraoral solitary titanium implants in terms of the flexible choice of mounting points and higher stability. Disadvantages become apparent in the complex individual intraoperative adaptation of the plate-based systems to the usually poorly accessible bone. The current article presents a method to overcome these disadvantages and make greater use of the advantages of plate-based systems.

Materials and methods: The bony midface of a patient who had undergone rhinectomy for cancer of the nasal entrance was reconstructed as a virtual 3D model based on preoperative CT. The open-source software, 3D Slicer allowed easy and fast reconstruction as well as adaptation for 3D printing using transparent plastic (MED610; stratasys Ltd., MN, USA).

Results: A titanium mini-plate (MEDICON) for anchoring the nasal prosthesis could be fitted extremely precisely on the midface 3D print. Important anatomical structures were spared, and screw placement was selected according to the individual bone thickness. Implantation of the in-advance fitted titanium plate was performed without complications and without further adjustments.

Conclusion: In-advance fitting of plate-based systems for anchorage of craniofacial prostheses using 3D printing of the midface overcomes their disadvantages of time-consuming and possibly imprecise individual adaptation. This method further exploits the advantages of higher stability through more possible mounting points, even in thinner bone, to prevent loosening. In addition, in-advance fitting of titanium plates on the 3D model enables better identification and protection of important anatomical structures and shortens operative time.

An Automatic Measurement System of Distal Femur Morphological Parameters Using 3D Slicer Software

Publication: Bone. 2022 Mar;156:116300. PMID: 34958998 | PDF

Authors: Chen Z, Wang Y, Li X, Wang K, Li Z, Yang P.

Institution: College of Computer Science, Xi'an University of Posts and Telecommunications, Shaanxi, China.

Abstract: In the field of joint surgery, the computer-aided design of knee prostheses suitable for the Chinese population requires a large quantity of anatomical knee data. In this study, we propose a new method that uses 3D Slicer software to automatically measure the morphological parameters of the distal femur. First, 141 femur samples were segmented from CT data to establish the femoral shape library. Next, balanced iterative reducing and clustering using hierarchies (BIRCH) combined with iterative closest point (ICP) and generalised procrustes analysis (GPA) were used to achieve fast registration of the femur samples. The statistical model was automatically calculated from the registered femur samples, and an orthopaedic surgeon marked the points on the statistical model. Finally, we developed an automatic measurement system using 3D Slicer software, and a deformable model matching method was applied to establish the point correspondence between the statistical model and the other samples. By matching points on the statistical model to corresponding points in other samples, we measured all other samples. We marked six points and measured eight parameters. We evaluated the performance of automatic matching by comparing the points marked manually with those matched automatically and verified the accuracy of the system by comparing the manual and automatic measurement results. The results indicated that the average error of the automatic matching points was 1.03 mm, and the average length error and average angle error measured automatically by the system were 0.37 mm and 0.63°, respectively. These errors were smaller than the intra-rater and inter-rater errors measured manually by two different surgeons, which showed that the accuracy of our automatic method was high. Taken together, this study established an accurate and automatic measurement system for the distal femur based on the secondary development of 3D Slicer software to assist orthopaedic surgeons in completing the measurements of big data and further promote the improved design of Chinese-specific knee prostheses.

Repeatability, Robustness, and Reproducibility of Texture Features on 3 Tesla Liver MRI

Publication: Clin Imaging. 2022 Mar;83:177-83. PMID: 35092926

Authors: Prabhu V, Gillingham N, Babb JS, Mali RD, Rusinek H, Bruno MT, Chandarana H.

Institution: Department of Radiology, NYU Langone Health, New York, NY, USA.

Abstract: Objective: Texture features are proposed for classification and prognostication, with lacking information about variability. We assessed 3 T liver MRI feature variability.

Methods: Five volunteers underwent standard 3 T MRI, and repeated with identical and altered parameters. Two readers placed regions of interest using 3D Slicer. Repeatability (between standard and repeat scan), robustness (between standard and parameter changed scan), and reproducibility (two reader variation) were computed using coefficient of variation (CV).

Results: 67%, 49%, and 61% of features had good-to-excellent (CV ≤ 10%) repeatability on ADC, T1, and T2, respectively, least frequently for first order (19-35%). 22%, 19%, and 21% of features had good-to-excellent robustness on ADC, T1, and T2, respectively. 52%, 35%, and 25% of feature measurements had good-to-excellent inter-reader reproducibility on ADC, T1, and T2, respectively, with highest good-to-excellent reproducibility for first order features on ADC/T1.

Conclusion: We demonstrated large variations in texture features on 3 T liver MRI. Further study should evaluate methods to reduce variability.

3D-Slicer Software-Assisted Neuroendoscopic Surgery in the Treatment of Hypertensive Cerebral Hemorrhage

Publication: Comput Math Methods Med. 2022 Feb 18;2022:7156598. PMID: 35222690 | PDF

Authors: Liao R, Liu L, Song B, Wan X, Wang S, Xu J.

Institution: University of Ulsan Department of Oral and Maxillofacial Surgery, Chungang University Hospital, Seoul, South Korea.

Abstract: To explore the 3D Slicer software-assisted endoscopic treatment for patients with hypertensive cerebral hemorrhage.

Methods: A total of 120 patients with hypertensive cerebral hemorrhage were selected and randomly divided into control group and 3D Slicer group with 60 cases each. Patients in the control group underwent traditional imaging positioning craniotomy, and patients in the 3D Slicer group underwent 3D Slicer followed by precision puncture treatment. In this paper, we evaluate the hematoma clearance rate, nerve function, ability of daily living, complication rate, and prognosis.

Results: The 3D Slicer group is better than the control group in various indicators. Compared with the control group, the 3D Slicer group has lower complications, slightly higher hematoma clearance rate, and better recovery of nerve function and daily living ability before and after surgery. The incidence of poor prognosis is low.

Conclusion: The 3D Slicer software-assisted endoscopic treatment for patients with hypertensive intracerebral hemorrhage has a better hematoma clearance effect, which is beneficial to the patient's early recovery and reduces the damage to the brain nerve of the patient.

Three-Dimensional Changes in the Mandibular Proximal Segment After Using a Surgery-First Approach in Patients With Class III Malocclusion and Facial Asymmetry

Publication: J Craniofac Surg. 2022 Feb 16. PMID: 35175981

Authors: Kim M, Jha N, Choi JH, Kim YJ, Lee U, Cevidanes L, Choi JY, Baek SH.

Institution: University of Ulsan Department of Oral and Maxillofacial Surgery, Chungang University Hospital, Seoul, South Korea.

Abstract: This study was performed to evaluate condylar position and angulation after asymmetric mandibular setback between a conventional (CA) and surgery-first approach (SFA) using three-dimensional analysis. The condylar positions of 30 patients with skeletal Class III malocclusion and facial asymmetry who underwent 1-jaw (sagittal split ramus osteotomy) or 2-jaw orthognathic surgery (Le Fort I osteotomy and sagittal split ramus osteotomy) with CA (n = 18) or SFA (n = 12) from 2 university hospitals were studied. The three-dimensional assessment of condylar changes was performed using computed tomography images at the initial time point (T0) and at least 6 months after surgery (T1). Segmentation of condyles and cranial base assessment from cone-beam computed tomography images were performed using ITK-SNAP software (version 3.4.0). Condylar position and angulation changes were calculated using 3D Slicer v. 4.10.2 software, and statistical analysis was performed. No significant translational or rotational condylar changes were observed between the deviated and nondeviated sides in each group or between the CA and SFA groups except yaw (P = 0.014). Linear mixed-model analysis and multivariate analysis showed no significant difference between the CA and SFA groups. Surgery-first approach might not be associated with more harmful effects on the condylar position and angulation changes as compared with CA.

FreeSurfer and 3D Slicer-Assisted SEEG Implantation for Drug-Resistant Epilepsy

Publication: Front Neurorobot. 2022 Feb 28;16:848746. PMID: 35295674. | PDF

Authors: Liu Q, Wang J, Wang C, Wei F, Zhang C, Wei H, Ye X, Xu J.

Institution: Department of Neurosurgery, Clinical Neuroscience Center Comprehensive Epilepsy Unit, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Abstract: Objective: Our study aimed to develop an approach to improve the speed and resolution of cerebral-hemisphere and lesion modeling and evaluate the advantages and disadvantages of robot-assisted surgical planning software.

Methods: We applied both conventional robot planning software (method 1) and open-source auxiliary software (FreeSurfer and 3D Slicer; method 2) to model the brain and lesions in 19 patients with drug-resistant epilepsy. The patients' mean age at implantation was 21.4 years (range, 6-52 years). Each patient received an average of 12 electrodes (range, 9-16) between May and November 2021. The electrode-implantation plan was designed based on the models established using the two methods. We statistically analyzed and compared the duration of designing the models and planning the implantation using these two methods and performed the surgeries with the implantation plan designed using the auxiliary software.

Results: A significantly longer time was needed to reconstruct a cerebral-hemisphere model using method 1 (mean, 206 s) than using method 2 (mean, 20 s) (p < 0.05). Both methods identified a mean of 1.4 lesions (range, 1-5) in each patient. Overall, using method 1 required longer (mean, 130 s; range, 48-436) than using method 2 (mean, 68.1 s; range, 50-104; p < 0.05). In addition, the clarity of the model based on method 1 was lower than that based on method 2. To devise an electrode-implantation plan, it took 9.1-25.5 min (mean, 16) and 6.6-14.8 min (mean, 10.2) based on methods 1 and 2, respectively (p < 0.05). The average target point error of 231 electrodes amounted to 1.90 mm ± 0.37 mm (range, 0.33-3.61 mm). The average entry point error was 0.89 ± 0.26 mm (range, 0.17-1.67 mm). None of the patients presented with intracranial hemorrhage or infection, and no other serious complications were observed.

Conclusions: FreeSurfer and 3D Slicer-assisted SEEG implantation is an excellent approach to enhance modeling speed and resolution, shorten the electrode-implantation planning time, and boost the efficiency of clinical work. These well-known, trusted open-source programs do not have explicitly restricted licenses. These tools, therefore, seem well suited for clinical-research applications under the premise of approval by an ethics committee, informed consent of the patient, and clinical judgment of the surgeon.

SegmentGeometry: A Tool for Measuring Second Moment of Area in 3D Slicer

Publication: Integr Org Biol. 2022 Feb 28;4(1):obac009. PMID: 35291672. | PDF

Authors: Huie JM, Summers AP, Kawano SM.

Institution: Department of Biological Sciences, George Washington University, Washington, DC, USA.

Abstract: Second moment of area is a measure of how well the cross-section of a beam will resist bending because of its shape. Many have used second moment of area to investigate the mechanical adaptations of biological structures from stingray jaws to animal limb bones. In this context it is important to acknowledge the assumptions of beam theory, in which second moment of area plays a key role, if reasonable results are desired. For example, to minimize shear the structure should be at least 10 times longer than it is wide and deflection should be minimal. Analyzing the internal geometry of biological structures has never been easier or more accessible given the wide, and growing availability of micro-CT scans. Here, we offer a guide on the care that needs to be taken when interpreting second moment of area, and present open-access, open-source software that can process hundreds if not thousands of structures in a short time frame. SegmentGeometry, an extension for the open-source imaging platform 3D Slicer, iterates slice-by-slice through 3D structures to calculate second moment of area and other cross-sectional properties. We analyzed 2 case studies to demonstrate the power of this tool and to highlight interpretations that can be gleaned from second moment of area. Second moment of area is just one part of the Euler-Bernoulli beam theory and considering the full equation would greatly increase the number and diversity of questions that can be answered.

Volumetric White Matter Hyperintensity Ranges Correspond to Fazekas Scores on Brain MRI

Publication: J Stroke Cerebrovasc Dis. 2022 Feb 11;31(4):106333. PMID: 35158149

Authors: Andere A, Jindal G, Molino J, Collins S, Merck D, Burton T, Stretz C, Yaghi S, Sacchetti DC, Jamal SE, Reznik ME, Furie K, Cutting S.

Institution: Department of Neurology, Brown University, Providence, RI, USA.

Abstract: Introduction: White matter hyperintensity (WMH) is an abnormal T2 signal in the deep and subcortical white matter visualized on MRI associated with hypertension, cerebrovascular disease, and aging. The Fazekas (Fz) scoring system is a commonly used qualitative tool to assess the severity of WMH. While studies have compared Fazekas scores to other scoring methods, the comparison of Fazekas scores and volume of WMH using current semiautomated volumetric techniques has not been studied.

Methods: We reviewed MRI studies acquired at our institution between 2015 and 2017. Relative WMH was scored by one author trained in Fazekas scoring. A board certified neuroradiologist scored them independently for confirmation. Manual segmentations of WMH were completed using 3D Slicer v.4.9. A 3D model was formed to quantify WMH in milliliters (mL). ANOVA tests were performed to determine the association of Fazekas scores with corresponding WMH volumes.

Results: Among the 198 patients in our study, WMH were visualized in 163 (Fz1: n=66; Fz2: n=49; Fz3: n=48). WMH volumes significantly differed according to Fazekas score (F = 141.1, p<0.001), with increasing WMHV associated with higher Fazekas scores: Fz1, range 0.1-8.3 mL (mean 3.7, SD 2.3); Fz2, range 6.0-17.7 mL (mean 10.8, SD 3.1); Fz3, range 14.2-77.2 mL (mean 35.2, SD 17.9); and Fz3 (excluding 11 outliers above 50 mL), 14.2-47.0 mL (mean 27.1, SD 8.9).

Conclusion: Fazekas scores correspond with distinct ranges of WMH volume with relatively little overlap, but scores based on volumes are more efficacious. A modified Fazekas from 0-4 should be considered.

A Radiomics Model Based on DCE-MRI and DWI May Improve the Prediction of Estimating IDH1 Mutation and Angiogenesis in Gliomas

Publication: Eur J Radiol. 2022 Feb;147:110141. PMID: 34995947

Authors: Wang J, Hu Y, Zhou X, Bao S, Chen Y, Ge M, Jia Z.

Institution: Department of Medical Imaging, Affiliated Hospital of Nantong University, Nantong, China.

Abstract: Purpose: To investigate the value of a radiomics model based on dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion weighted imaging (DWI) in estimating isocitrate dehydrogenase 1 (IDH1) mutation and angiogenesis in gliomas.

Method: One hundred glioma patients with DCE-MRI and DWI were enrolled in this study (training and validation groups with a ratio of 7:3). The IDH1 genotypes and expression of vascular endothelial growth factor (VEGF) in gliomas were assessed by immunohistochemistry. Radiomics features were extracted by an open source software 3D Slicer and reduced using Least absolute shrinkage and selection operator (Lasso). The support vector machine (SVM) model was developed based on the most useful predictive radiomics features. The conventional model was built by the selected clinical and morphological features. Finally, a combined model including radiomics signature, age and enhancement degree was established. Receiver operator characteristic (ROC) curve was implemented to assess the diagnostic performance of the three models.

Results: For IDH1 mutation, the combined model achieved the highest area under curve (AUC) in comparison with the SVM and conventional models (training group, AUC = 0.967, 0.939 and 0.906; validation group, AUC = 0.909, 0.880 and 0.842). Furthermore, the SVM model showed good diagnostic performance in estimating gliomas VEGF expression (validation group, AUC = 0.919).

Conclusions: The radiomics model based on DCE-MRI and DWI can have a considerable effect on the evaluation of IDH1 mutation and angiogenesis in gliomas.

The Role of Pre-therapeutic 18F-FDG PET/CT in Pediatric Hemophagocytic Lymphohistiocytosis With Epstein-Barr Virus Infection

Publication: Front Med (Lausanne). 2022 Jan 21;8:836438. PMID: 35127776 | PDF

Authors: Lu X, Wei A, Yang X, Liu J, Li S, Kan Y, Wang W, Wang T, Zhang R, Yang J.

Institution: Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China.

Abstract: Objective: To evaluate the role of pre-therapeutic 18F-FDG PET/CT in pediatric hemophagocytic lymphohistiocytosis (HLH) with Epstein-Barr virus (EBV) infection.

Methods: This retrospective study included 29 HLH children (1-16 years) with EBV infection, who underwent pre-therapeutic 18F-FDG PET/CT from July 2018 to November 2020. Pathology results were considered as the reference standard. These patients were divided into two groups: EBV-induced malignancy-associated HLH (M-HLH, N = 9) and EBV-induced non-malignancy-associated HLH (NM-HLH, N = 20). The regions of interest (ROIs) of the liver, spleen (Sp), bone marrow (BM), lymph nodes (LN), hypermetabolic lesions, liver background (LiBG), and mediastinum (M) were drawn with software 3D Slicer. The volumetric and metabolic parameters, including maximum standard uptake value (SUVmax), metabolic tumor volume, and total lesion glycolysis of these ROIs, clinical parameters, and laboratory parameters were compared between the two groups. The efficiency of the above parameters in predicting the treatment response and overall survival (OS) was analyzed.

Results: Receiver operating characteristic curve analysis indicated that SUVmax-lesions and SUVmax-LN/M (AUC = 0.822, 0.819, cut-off = 6.04, 5.74, respectively) performed better in differentiating M-HLH from NM-HLH. It had the best diagnostic performance when age was added with the SUVmax-LN/M (AUC = 0.933, sensitivity = 100%, specificity = 85.0%). The presence of extranodal hypermetabolic lesions in multiple organs indicated the M-HLH (P = 0.022). Older age, higher SUVmax-LN and SUVmax-lesions, and the presence of serous effusion were associated with poorer treatment response at the 2nd and 4th week (not reaching partial remission). Multivariate analysis showed that SUVmax-lesions > 7.66 and SUVmax-Sp/LiBG > 2.01 were independent prognostic factors for overall survival (P = 0.025, 0.036, respectively).

Conclusions: 18F-FDG PET/CT could be a valuable technique for identifying the underlying malignancy and predicting prognosis in pediatric HLH with EBV infection. M-HLH could be considered when SUVmax-lesions > 6.04, SUVmax-LN/M > 5.74, and the presence of extranodal hypermetabolic lesions in multiple organs on 18F-FDG PET/CT. SUVmax-lesions and SUVmax-Sp/LiBG might be independent prognostic factors for OS.

Total Intracranial Volume as a Covariate for Predicting Prognosis in Patients With Primary Intracerebral Hemorrhage

Publication: Clin Neurol Neurosurg. 2022 Jan 17;214:107135. PMID: 35121234

Authors: Wang L, Liu C, Lu E, Zhang D, Zhang H, Xu X, Liu R, Yuan C, Sun J, Zhou Q, Chen X, Wang L, Yang G.

Institution: Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.

Abstract: Objectives: The initial hematoma volume is reliable and stable imaging predictor for the outcome of patients with intracerebral hemorrhage, and the total intracranial volume varies between patients. However, the role of total intracranial volume in predicting the prognosis of spontaneous intracerebral hemorrhage has not been previously addressed.

Methods: 782 patients with spontaneous intracerebral hemorrhage were selected in this retrospective cohort at the Neurosurgery Emergency Unit of The First Affiliated Hospital of Harbin Medical University. Due to missing CT images, initial CT exceeding 24 h, traumatic cerebral hemorrhage, and aneurysm, 145 patients were excluded and the remaining 637 patients were included in our analysis. Functional outcome was assessed using the modified Rankin Scale(mRS) and mortality at 3-months after spontaneous intracerebral hemorrhage. CT image datasets were calculated by 3D Slicer. The initial hematoma volume was normalized to the total intracranial volume to evaluate poor functional outcomes (mRS, 4-6) and mortality.

Results: The results demonstrated that normalized initial hematoma volume can be used as an indicator of poor functional outcome (mRS, 4-6) (AUCNrIHV=0.753, 95%-CI:0.710-0.795, p < 0.001), mortality (AUCNrIHV=0.808, 95%-CI:0.754-0.862, p < 0.001) and hematoma expansion (AUCNrIHV=0.690, 95%-CI:0.613-0.767, p < 0.001). Meanwhile, the initial hematoma volume in predicting poor functional outcome (AUCIHV=0.749, 95%-CI:0.707-0.792, p < 0.001), mortality (AUCIHV=0.816, 95%-CI: 0.763-0.870, p < 0.001) and hematoma expansion (AUCIHV=0.704, 95%-CI: 0.626-0.782, p < 0.001) was similar to the normalized initial hematoma volume.

Conclusions: The normalized initial hematoma volume has no apparent benefit in predicting the prognosis of patients with cerebral hemorrhage compared with initial hematoma volume.

A Preoperative MRI-Based Radiomics-Clinicopathological Classifier to Predict the Recurrence of Pituitary Macroadenoma Within 5 Years

Publication: Front Neurol. 2022 Jan 5;12:780628. PMID: 35069413 | PDF

Authors: Zhang Y, Luo Y, Kong X, Wan T, Long Y, Ma J.

Institution: Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.

Abstract: To investigate the ability of a MRI-based radiomics-clinicopathological model to predict pituitary macroadenoma (PMA) recurrence within 5 years. Materials and Methods: We recruited 74 recurrent and 94 non-recurrent subjects, following first surgery with 5-year follow-up data. Univariate and multivariate analyses were conducted to identify independent clinicopathological risk factors. Two independent and blinded neuroradiologists used 3D Slicer software to manually delineate whole tumors using preoperative axial contrast-enhanced T1WI (CE-T1WI) images. 3D Slicer was then used to extract radiomics features from segmented tumors. Dimensionality reduction was carried out by the least absolute shrinkage and selection operator (LASSO). Two multilayer perceptron (MLP) models were established, including independent clinicopathological risk factors (Model 1) and a combination of screened radiomics features and independent clinicopathological markers (Model 2). The predictive performance of these models was evaluated by receiver operator characteristic (ROC) curve analysis. Results: In total, 1,130 features were identified, and 4 of these were selected by LASSO. In the test set, the area under the curve (AUC) of Model 2 was superior to Model 1 {0.783, [95% confidence interval (CI): 0.718-.860] vs. 0.739, (95% CI: 0.665-0.818)}. Model 2 also yielded the higher accuracy (0.808 vs. 0.692), sensitivity (0.826 vs. 0.652), and specificity (0.793 vs. 0.724) than Model 1. Conclusions: The integrated classifier was superior to a clinical classifier and may facilitate the prediction of individualized prognosis and therapy.

Accuracy of Patient Setup Positioning Using Surface-Guided Radiotherapy With Deformable Registration in Cases of Surface Deformation

Publication: J Appl Clin Med Phys. 2022 Jan 25;e13493. PMID: 35077004

Authors: Kadman B, Takemura A, Ito T, Okada N, Kojima H, Ueda S.

Institution: Division of Health Sciences, Graduate School of Medical Sciences, Pharmaceutical and Health Sciences, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Japan.

Abstract: The Catalyst™ HD (C-RAD Positioning AB, Uppsala, Sweden) is surface-guided radiotherapy (SGRT) equipment that adopts a deformable model. The challenge in applying the SGRT system is accurately correcting the setup error using a deformable model when the body of the patient is deformed. This study evaluated the effect of breast deformation on the accuracy of the setup correction of the SGRT system. Physical breast phantoms were used to investigate the relationship between the mean deviation setup error obtained from the SGRT system and the breast deformation. Physical breast phantoms were used to simulate extension and shrinkage deformation (-30 to 30 mm) by changing breast pieces. 3D Slicer software was used to evaluate the deformation. The maximum deformations in X, Y, and Z directions were obtained as the differences between the original and deformed breasts. We collected the mean deviation setup error from the SGRT system by replacing the original breast part with the deformed breast part. The mean absolute difference of lateral, longitudinal, vertical, pitch, roll, and yaw, between the rigid and deformable registrations was 2.4 ± 1.7 mm, 1.3 ± 1.2 mm, 6.4 ± 5.2 mm, 2.5° ± 2.5°, 2.2° ± 2.4°, and 1.0° ± 1.0°, respectively. Deformation in the Y direction had the best correlation with the mean deviation translation error (R = 0.949) and rotation error (R = 0.832). As the magnitude of breast deformation increased, both mean deviation setup errors increased, and there was greater error in translation than in rotation. Large deformation of the breast surface affects the setup correction. Deformation in the Y direction most affects translation and rotation errors.

Spatial Omics: Navigating to the Golden Era of Cancer Research

Publication: Clin Transl Med. 2022 Jan;12(1):e696. PMID: 35040595 | PDF

Authors: Wu Y, Cheng Y, Wang X, Fan J, Gao Q.

Institution: Center for Tumor Diagnosis & Therapy and Department of Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China.

Abstract: The idea that tumour microenvironment (TME) is organised in a spatial manner will not surprise many cancer biologists; however, systematically capturing spatial architecture of TME is still not possible until recent decade. The past five years have witnessed a boom in the research of high-throughput spatial techniques and algorithms to delineate TME at an unprecedented level. Here, we review the technological progress of spatial omics and how advanced computation methods boost multi-modal spatial data analysis. Then, we discussed the potential clinical translations of spatial omics research in precision oncology, and proposed a transfer of spatial ecological principles to cancer biology in spatial data interpretation. So far, spatial omics is placing us in the golden age of spatial cancer research. Further development and application of spatial omics may lead to a comprehensive decoding of the TME ecosystem and bring the current spatiotemporal molecular medical research into an entirely new paradigm.

"Computational strategies originally designed for radiomics, such as 3D Slicer, are expected to reconstruct the spatial molecular organization."

WHO Grade Loses Its Prognostic Value in Molecularly Defined Diffuse Lower-Grade Gliomas

Publication: Front Oncol. 2022 Jan 10;11:803975. PMID: 35083156 | PDF

Authors: Carstam L, Corell A, Smits A, Dénes A, Barchéus H, Modin K, Sjögren H, Ferreyra Vega S, Bontell TO, Carén H, Jakola AS.

Institution: Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden.

Abstract: Background: While molecular insights to diffuse lower-grade glioma (dLGG) have improved the basis for prognostication, most established clinical prognostic factors come from the pre-molecular era. For instance, WHO grade as a predictor for survival in dLGG with isocitrate dehydrogenase (IDH) mutation has recently been questioned. We studied the prognostic role of WHO grade in molecularly defined subgroups and evaluated earlier used prognostic factors in the current molecular setting.

Material and methods: A total of 253 adults with morphological dLGG, consecutively included between 2007 and 2018, were assessed. IDH mutations, codeletion of chromosomal arms 1p/19q, and cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) deletions were analyzed.

Results: There was no survival benefit for patients with WHO grade 2 over grade 3 IDH-mut dLGG after exclusion of tumors with known CDKN2A/B homozygous deletion (n=157) (log-rank p=0.97). This was true also after stratification for oncological postoperative treatment and when astrocytomas and oligodendrogliomas were analyzed separately. In IDH-mut astrocytomas, residual tumor volume after surgery was an independent prognostic factor for survival (HR 1.02; 95% CI 1.01-1.03; p=0.003), but not in oligodendrogliomas (HR 1.02; 95% CI 1.00-1.03; p=0.15). Preoperative tumor size was an independent predictor in both astrocytomas (HR 1.03; 95% CI 1.00-1.05; p=0.02) and oligodendrogliomas (HR 1.05; 95% CI 1.01-1.09; p=0.01). Age was not a significant prognostic factor in multivariable analyses (astrocytomas p=0.64, oligodendrogliomas p=0.08).

Conclusion: Our findings suggest that WHO grade is not a robust prognostic factor in molecularly well-defined dLGG. Preoperative tumor size remained a prognostic factor in both IDH-mut astrocytomas and oligodendrogliomas in our cohort, whereas residual tumor volume predicted prognosis in IDH-mut astrocytomas only. The age cutoffs for determining high risk in patients with IDH-mut dLGG from the pre-molecular era are not supported by our results.

Keywords: CDKN2A/B deletion; IDH-mut; WHO grade; astrocytoma; extent of resection; lower-grade glioma; oligodendroglioma; prognostic factors.

"The volume of residual tumor after surgery was determined by tumor volume segmentation. The tumor volume was evaluated by semi-automatic segmentation performed with the open-source software 3D Slicer, v.4.6.2 or newer."

A Baboon Brain Atlas for Magnetic Resonance Imaging and Positron Emission Tomography Image Analysis

Publication: Front Neuroanat. 2022 Jan 14;15:778769. PMID: 35095430 | PDF

Authors: Agaronyan A, Syed R, Kim R, Hsu CH, Love SA, Hooker JM, Reid AE, Wang PC, Ishibashi N, Kang Y, Tu TW.

Institution: Center for Neuroscience Research, Children's National Hospital, Washington D.C., USA.

Abstract: The olive baboon (Papio anubis) is phylogenetically proximal to humans. Investigation into the baboon brain has shed light on the function and organization of the human brain, as well as on the mechanistic insights of neurological disorders such as Alzheimer's and Parkinson's. Non-invasive brain imaging, including positron emission tomography (PET) and magnetic resonance imaging (MRI), are the primary outcome measures frequently used in baboon studies. PET functional imaging has long been used to study cerebral metabolic processes, though it lacks clear and reliable anatomical information. In contrast, MRI provides a clear definition of soft tissue with high resolution and contrast to distinguish brain pathology and anatomy, but lacks specific markers of neuroreceptors and/or neurometabolites. There is a need to create a brain atlas that combines the anatomical and functional/neurochemical data independently available from MRI and PET. For this purpose, a three-dimensional atlas of the olive baboon brain was developed to enable multimodal imaging analysis. The atlas was created on a population-representative template encompassing 89 baboon brains. The atlas defines 24 brain regions, including the thalamus, cerebral cortex, putamen, corpus callosum, and insula. The atlas was evaluated with four MRI images and 20 PET images employing the radiotracers for [11C]benzamide, [11C]metergoline, [18F]FAHA, and [11C]rolipram, with and without structural aids like [18F]flurodeoxyglycose images. The atlas-based analysis pipeline includes automated segmentation, registration, quantification of region volume, the volume of distribution, and standardized uptake value. Results showed that, in comparison to PET analysis utilizing the "gold standard" manual quantification by neuroscientists, the performance of the atlas-based analysis was at >80 and >70% agreement for MRI and PET, respectively. The atlas can serve as a foundation for further refinement, and incorporation into a high-throughput workflow of baboon PET and MRI data. The new atlas is freely available on the Figshare online repository (https://doi.org/10.6084/m9.figshare.16663339), and the template images are available from neuroImaging tools & resources collaboratory (NITRC) (https://www.nitrc.org/projects/haiko89/).

"Each PET image was registered to the atlas by 3D Slicer’s landmark registration tool "

SPHARM-PDM Based Image Preprocessing Pipeline for Quantitative Morphometric Analysis (QMA) for in Situ Joint Assessment in Rabbit and Rat Models

Publication: Sci Rep. 2022 Jan 21;12(1):1113. PMID: 35064147 | PDF

Authors: Durongbhan P, Davey CE, Stok KS.

Institution: Department of Biomedical Engineering, The University of Melbourne, Australia.

Abstract: The accessibility of quantitative measurements of joint morphometry depends on appropriate tibial alignment and volume of interest (VOI) selection of joint compartments; often a challenging and time-consuming manual task. In this work, we developed a novel automatic, efficient, and model-invariant image preprocessing pipeline that allows for highly reproducible 3D quantitative morphometric analysis (QMA) of the joint. The pipeline addresses the problem by deploying two modules: an alignment module and a subdivision module. Alignment is achieved by representing the tibia in its basic form using lower degree spherical harmonic basis functions and aligning using principal component analysis. The second module subdivides the joint into lateral and medial VOIs via a watershedding approach based on persistence homology. Multiple repeated micro-computed tomography scans of small (rat) and medium (rabbit) animal knees were processed using the pipeline to demonstrate model invariance. Existing QMA was performed to evaluate the pipeline's ability to generate reproducible measurements. Intraclass correlation coefficient and mean-normalised root-mean-squared error of more than 0.75 and lower than 9.5%, respectively, were achieved for joint centre of mass, joint contact area under virtual loading, joint space width, and joint space volume. Processing time and technical requirements were reduced compared to manual processing in previous studies.

"SPHARM processing, statistical shape analysis module in 3D Slicer)"

Clinical Evaluation of 3D Printed Nano-Porous Hydroxyapatite Bone Graft for Alveolar Ridge Preservation: A Randomized Controlled Trial

Publication: J Dent Sci. 2022 Jan;17(1):194-203. PMID: 35028038 | PDF

Authors: Kijartorn P, Wongpairojpanich J, Thammarakcharoen F, Suwanprateeb J, Buranawat B.

Institution: Department of Periodontology and Implantology, Faculty of Dentistry, Thammasat University, Pathum Thani, Thailand.

Abstract: Background/purpose: Ridge resorption after tooth extraction may result in inadequate bone volume and unfavorable ridge architecture for ideal implant placement. The use of bone substitutes has been advocated to fill extraction sites and to enhance primary implant stability. This study was made to evaluate the clinical efficacy of novel 3D printed nano-porous hydroxyapatite (3DP HA, test group) in comparison to nano-crystalline bone graft (NanoBone®, control group) in alveolar ridge preservation prior to implant placement.

Materials and methods: Thirty patients were randomized into two groups following tooth extraction. All extracted sockets were filled with 3DP HA or NanoBone® and covered with a non-resorbable membrane. After four months, cone-beam computed tomography (CBCT) and intraoral scanner were used to measure dimensional changes of bone and soft tissue surface. Bone core specimens were harvested for histological analysis during implant osteotomy. Implant stability was assessed using a modified damping capacity analysis.

Results: At four months postoperatively, dimensional changes in soft tissue surface resorption were less in the test group than in the control group; however, alveolar bone resorption was the same in both groups. Histological analysis revealed new bone formation, residual graft and fibrous connective tissue in both groups. The average primary implant stability (IST) value for both groups was approximately 70. There was no statistically significant difference in all parameters between two groups (p > 0.05).

Conclusion: 3DP HA could potentially be used as an alternative bone graft material for alveolar ridge preservation.

"To measure the alveolar bone changes, two DICOM files acquired from CBCT from two time points were segmented and reconstructed into 3D STL image files by using 3D Slicer software v.4.10.1."

High-Resolution MRI of the Human Palatine Tonsil and Its Schematic Anatomic 3D Reconstruction

Publication: J Anat. 2022 Jan;240(1):166-71. PMID: 34342906 | PDF

Authors: Herrmann KH, Hoffmann F, Ernst G, Pertzborn D, Pelzel D, Geißler K, Guntinas-Lichius O, Reichenbach JR, von Eggeling F.

Institution: Medical Physics Group, Institute for Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany.

Abstract: The palatine tonsils form an important part of the human immune system. Together with the other lymphoid tonsils of Waldeyer's tonsillar ring, they act as the first line of defense against ingested or inhaled pathogens. Although histologically stained sections of the palatine tonsil are widely available, they represent the tissue only in two dimensions and do not provide reference to three-dimensional space. Such a representation of a tonsillar specimen based on imaging data as a 3D anatomical reconstruction is lacking both in scientific publications and especially in textbooks. As a first step in this direction, the objective of the present work was to image a resected tonsil specimen with high spatial resolution in a 9.4 T small-bore pre-clinical MRI and to combine these data with data from the completely sectioned and H&E stained same palatine tonsil. Based on the information from both image modalities, a 3D anatomical sketch was drawn by a scientific graphic artist. In perspective, such studies could help to overcome the difficulty of capturing the spatial extent and arrangement of anatomical structures from 2D images and to establish a link between three-dimensional anatomical preparations and two-dimensional sections or illustrations, as they have been found so far in common textbooks and anatomical atlases.

"3D model was assembled using the free software tool, 3D Slicer"

The Effects of Cranial Orientation on Forensic Frontal Sinus Identification as Assessed by Outline Analyses

Publication: Clin Transl Med. 2022 Jan;12(1):e696. PMID: 35053060 | PDF

Authors: Butaric LN, Richman A, Garvin HM.

Institution: Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA, USA.

Abstract: The utility of frontal sinuses for personal identification is widely recognized, but potential factors affecting its reliability remain uncertain. Deviations in cranial position between antemortem and postmortem radiographs may affect sinus appearance. This study investigates how slight deviations in orientations affect sinus size and outline shape and potentially impact identification. Frontal sinus models were created from CT scans of 21 individuals and digitally oriented to represent three clinically relevant radiographic views. From each standard view, model orientations were deviated at 5° intervals in horizontal, vertical, and diagonal (e.g., left-up) directions (27 orientations per individual). For each orientation, sinus dimensions were obtained, and outline shape was assessed by elliptical Fourier analyses and principal component (PC) analyses. Wilcoxon sign rank tests indicated that sinus breadth remained relatively stable (p > 0.05), while sinus height was significantly affected with vertical deviations (p < 0.006). Mann-Whitney U tests on Euclidean distances from the PC scores indicated consistently lower intra- versus inter-individual distances (p < 0.05). Two of the three orientations maintained perfect (100%) outline identification matches, while the third had a 98% match rate. Smaller and/or discontinuous sinuses were most problematic, and although match rates are high, practitioners should be aware of possible alterations in sinus variables when conducting frontal sinus identifications.

"The associated frontal sinus and cranial models for each individual were imported into the program 3D Slicer."

Phenotyping Type 2 Diabetes in Terms of Myocardial Insulin Resistance and Its Potential Cardiovascular Consequences: A New Strategy Based on 18 F-FDG PET/CT

Publication: J Pers Med. 2022 Jan 2;12(1):30. PMID: 35055345 | PDF

Authors: Herance JR, Simó R, Velasquez MA, Paun B, García-Leon D, Aparicio C, Marés R, Simó-Servat O, Castell-Conesa J, Hernández C, Aguadé-Bruix S.

Institution: Medical Molecular Imaging Research Group, Nuclear Medicine Department, Vall d'Hebron Research Institute (VHIR), Vall d'Hebron University Hospital, Autonomous University Barcelona, Barcelona, Spain.

Abstract: Background: Systemic insulin resistance is generally postulated as an independent risk factor of cardiovascular events in type 2 diabetes (T2D). However, the role of myocardial insulin resistance (mIR) remains to be clarified.

Methods: Two 18F-FDG PET/CT scans were performed on forty-three T2D patients at baseline and after hyperinsulinemic-euglycemic clamp (HEC). Myocardial insulin sensitivity (mIS) was determined by measuring the increment in myocardial 18F-FDG uptake after HEC. Coronary artery calcium scoring (CACs) and myocardial radiodensity (mRD) were assessed by CT.

Results: After HEC, seventeen patients exhibited a strikingly enhancement of myocardial 18F-FDG uptake and twenty-six a marginal increase, thus revealing mIS and mIR, respectively. Patients with mIR showed higher mRD (HU: 38.95 [33.81-44.06] vs. 30.82 [21.48-38.02]; p = 0.03) and CACs > 400 (AU: 52% vs. 29%; p = 0.002) than patients with mIS. In addition, HOMA-IR and mIS only showed a correlation in those patients with mIR.

Conclusions: 18F-FDG PET combined with HEC is a reliable method for identifying patients with mIR. This subgroup of patients was found to be specifically at high risk of developing cardiovascular events and showed myocardial structural changes. Moreover, the gold-standard HOMA-IR index was only associated with mIR in this subgroup of patients. Our results open up a new avenue for stratifying patients with cardiovascular risk in T2D.

"All acquired 18F-FDG PET images in DICOM format were first SUVbw normalized using the PET DICOM Extension available in 3D Slicer."

Developing Virtual Reality Head Mounted Display (HMD) Set-Up for Thoracoscopic Surgery of Complex Congenital Lung MalFormations in Children

Publication: Children (Basel). 2022 Jan 3;9(1):50. PMID: 35053675 | PDF

Authors: Pelizzo G, Costanzo S, Roveri M, Lanfranchi G, Vertemati M, Milani P, Zuccotti G, Cassin S, Panfili S, Rizzetto F, Campari A, Camporesi A, Calcaterra V.

Institution: Pediatric Surgery Department, "Vittore Buzzi" Children's Hospital, Milan, Italy.

Abstract: Video assisted thoracoscopic surgery (VATS) has been adopted in pediatric age for the treatment of congenital lung malformations (CLM). The success of VATS in pediatrics largely depends on the surgeon's skill ability to understand the airways, vascular system and lung parenchyma anatomy in CLM. In the last years, virtual reality (VR) and 3-dimensional (3D) printing of organ models and VR head mounted display (HMD) technologies have been introduced for completion of preoperative planning in adult patients. To date no reports about the use of VR HMD technologies in a pediatric setting are available. The aim of this report is to introduce a VR HMD model in VATS procedure to improve the quality of care in children with CLM. VR HMD set-up for planning thoracoscopic surgery was performed in a series of pediatric patients with diagnosis of CLM. The preoperative VR HMD evaluation allowed a navigation into the malformation with the aim to explore, interact, and make the surgeon more confident and skilled to answer to the traps. A development of surgical simulations models and teaching program dedicated to education and training in pediatric VATS is suitable among the pediatric surgery community. Further studies should demonstrate all the benefits of such technology in pediatric patients submitted to VATS procedure.

"CT images were then exported into DICOM files and loaded into 3D Slicer."

Dynamic Contrast-Enhanced Magnetic Resonance Imaging for the Prediction of Monoclonal Antibody Tumor Disposition

Publication: Int J Mol Sci. 2022 Jan 8;23(2):679. PMID: 35054865 | PDF

Authors: Bordeau BM, Polli JR, Schweser F, Grimm HP, Richter WF, Balthasar JP.

Institution: Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.

Abstract: The prediction of monoclonal antibody (mAb) disposition within solid tumors for individual patients is difficult due to inter-patient variability in tumor physiology. Improved a priori prediction of mAb pharmacokinetics in tumors may facilitate the development of patient-specific dosing protocols and facilitate improved selection of patients for treatment with anti-cancer mAb. Here, we report the use of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), with tumor penetration of the contrast agent gadobutrol used as a surrogate, to improve physiologically based pharmacokinetic model (PBPK) predictions of cetuximab pharmacokinetics in epidermal growth factor receptor (EGFR) positive xenografts. In the initial investigations, mice bearing Panc-1, NCI-N87, and LS174T xenografts underwent DCE-MRI imaging with the contrast agent gadobutrol, followed by intravenous dosing of an 125Iodine-labeled, non-binding mAb (8C2). Tumor concentrations of 8C2 were determined following the euthanasia of mice (3 h-6 days after 8C2 dosing). Potential predictor relationships between DCE-MRI kinetic parameters and 8C2 PBPK parameters were evaluated through covariate modeling. The addition of the DCE-MRI parameter Ktrans alone or Ktrans in combination with the DCE-MRI parameter Vp on the PBPK parameters for tumor blood flow (QTU) and tumor vasculature permeability (σTUV) led to the most significant improvement in the characterization of 8C2 pharmacokinetics in individual tumors. To test the utility of the DCE-MRI covariates on a priori prediction of the disposition of mAb with high-affinity tumor binding, a second group of tumor-bearing mice underwent DCE-MRI imaging with gadobutrol, followed by the administration of 125Iodine-labeled cetuximab (a high-affinity anti-EGFR mAb). The MRI-PBPK covariate relationships, which were established with the untargeted antibody 8C2, were implemented into the PBPK model with considerations for EGFR expression and cetuximab-EGFR interaction to predict the disposition of cetuximab in individual tumors (a priori). The incorporation of the Ktrans MRI parameter as a covariate on the PBPK parameters QTU and σTUV decreased the PBPK model prediction error for cetuximab tumor pharmacokinetics from 223.71 to 65.02%. DCE-MRI may be a useful clinical tool in improving the prediction of antibody pharmacokinetics in solid tumors. Further studies are warranted to evaluate the utility of the DCE-MRI approach to additional mAbs and additional drug modalities.

"Dynamic contrast-enhanced scans were opened in 3D Slicer, and tumor regions were defined using the segmentation editor."

Distribution of Electric Field in Patients With Obsessive Compulsive Disorder Treated With Deep Brain Stimulation of the Bed Nucleus of Stria Terminalis

Publication: Acta Neurochir (Wien). 2022 Jan;164(1):193-202 PMID: 34652518 | PDF

Authors: Naesström M, Johansson J, Hariz M, Bodlund O, Wårdell K, Blomstedt P.

Institution: Division of Psychiatry, Department of Clinical Sciences, Umea University, Umea, Sweden

Abstract: Background: Deep brain stimulation (DBS) is being investigated as a treatment for therapy-refractory obsessive compulsive disorder (OCD). Many different brain targets are being trialled. Several of these targets such as the ventral striatum (including the nucleus accumbens (NAc)), the ventral capsule, the inferior thalamic peduncle, and the bed nucleus of stria terminalis (BNST)) belong to the same network, are anatomically very close to one another, or even overlap. Data is still missing on how various stimulation parameters in a given target will affect surrounding anatomical areas and impact the clinical outcome of DBS.

Methods: In a pilot study of eleven participants with DBS of the BNST, we investigate through patient-specific simulation of electric field, which anatomical areas are affected by the electric field, and if this can be related to the clinical results. Our study combined individual patient's stimulation parameters at 12- and 24-month follow-up with image data from the preoperative MRI and postoperative CT. These data were used to calculate the distribution of electric field and create individual anatomical models of the field of stimulation.

Results: The individual electric stimulation fields by stimulation in the BNST were similar at both the 12- and 24-month follow-up, involving mainly anterior limb of the internal capsule (ALIC), genu of the internal capsule (IC), BNST, fornix, anteromedial globus pallidus externa (GPe), and the anterior commissure. A statistical significant correlation (p < 0.05) between clinical effect measured by the Yale-Brown Obsessive Compulsive Scale and stimulation was found at the 12-month follow-up in the ventral ALIC and anteromedial GPe.

Conclusions: Many of the targets under investigation for OCD are in anatomical proximity. As seen in our study, off-target effects are overlapping. Therefore, DBS in the region of ALIC, NAc, and BNST may perhaps be considered to be stimulation of the same target.

"The results were visualized in 3D Slicer v.4.6.2"

Finite Element Analysis in Clinical Patients With Atherosclerosis

Publication: J Mech Behav Biomed Mater. 2022 Jan;125:104927. PMID: 34740008

Authors: Noble C, Carlson KD, Neumann E, Lewis B, Dragomir-Daescu D, Lerman A, Erdemir A, Young MD.

Institution: Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.

Abstract: Endovascular plaque composition is strongly related to stent strut stress and is responsible for strut fatigue, stent failure, and possible in-stent restenosis. To evaluate the effect of plaque on artery wall resistance to expansion we performed in silico analysis of atherosclerotic vessels. We generated finite element models from in vivo intravascular ultrasound virtual histology images to determine local artery surface stiffness and determined which plaque structures have the greatest influence. We validated the predictive capacity of our modeling approach by testing an atherosclerotic peripheral artery ex vivo with pressure-inflation testing at physiological pressures ranging from 10 to 200 mmHg. For this purpose, the in silico deformation of the arterial wall was compared to that observed ex vivo. We found that calcification had a positive effect on surface stiffness with fibrous plaque and necrotic core having negative effects. Additionally, larger plaque structures demonstrated significantly higher average surface stiffness and calcification located nearer the lumen was also shown to increase surface stiffness. Therefore, more developed plaques will have greater resistance to expansion and higher stent strut stress, with calcification located near the lumen further increasing stress in localized areas. Thus, it may be expected that such plaque structures may increase the likelihood of localized stent strut fracture.

"Using the segment editor module in 3D Slicer, the high intensity pixels (representing primarily the artery wall) were segmented using the “threshold” effect."

Predictive Value of Thrombus Susceptibility for Cardioembolic Stroke by Quantitative Susceptibility Mapping

Publication: Quant Imaging Med Surg. 2022 Jan;12(1):550-7. PMID: 34993100 | PDF

Authors: Chen J, Zhang Z, Nie X, Xu Y, Liu C, Zhao X, Wang Y.

Institution: Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.

Abstract: Background: The hypointense blooming signal of thrombi on susceptibility-weighted imaging (SWI), known as the susceptibility vessel sign (SVS), is predictive of cardioembolic stroke. The SVS originates from the local magnetic susceptibility effect; thus, the susceptibility value of thrombi may provide useful information in discriminating stroke etiology. We aim to utilize quantitative susceptibility mapping (QSM) to assess thrombus's susceptibility value in acute ischemic stroke patients and explore the relationship of thrombus susceptibility with cardioembolic stroke.

Methods: From 2018 to 2020, 132 consecutive acute ischemic stroke patients with middle cerebral artery occlusion were recruited within 48 hours of onset. All patients underwent a three-dimensional multi-echo SWI scan using a 3 Tesla magnetic resonance imaging scanner. The SVS presence and the diameter of the SVS-related hypointense signal were assessed on SWI. QSM was applied to compute the susceptibility value of the thrombus. The receiver operating characteristic (ROC) methodology was used to define the optimal cutoff value of the susceptibility in QSM and the diameter on SWI for predicting cardioembolic stroke.

Results: The SVS was identified in 93 (70.5%) patients with symptomatic middle cerebral artery occlusion and was significantly associated with cardioembolism. The hyperintense signal on QSM in the corresponding middle cerebral artery occlusion was present in 116 (87.9%) patients. ROC analysis indicated that thrombus susceptibility had a greater area under the curve than that of the SVS diameter (0.88 vs. 0.70, P<0.001) and that the optimal cutoff value of thrombus susceptibility for cardioembolism was 0.35 ppm. Multivariate analysis demonstrated that thrombus susceptibility (≥0.35 ppm) was an independent predictor of cardioembolic stroke (odds ratio =20.75; 95% CI, 7.19-59.87; P<0.001), with sensitivity, specificity, a positive predictive value, and a negative predictive value of 85.2%, 80.8%, 75.4%, and 88.7%, respectively, while the SVS presence showed sensitivity, specificity, a positive predictive value, and a negative predictive value of 90.7%, 43.6%, 87.2%, and 52.7%, respectively.

Conclusions: Thrombus susceptibility provides superior diagnostic performance over the SVS for discriminating between cardioembolism and other stroke subtypes. Quantitative susceptibility measurements of thrombi may help predict cardioembolic stroke in patients with acute middle cerebral artery occlusion.

"The thrombus susceptibility value [in units of parts per million (ppm)] and thrombus volume of the ROIs were extracted using the 3D Slicer quantification module."

Knee Joint Unloading and Daily Physical Activity Associate With Cartilage T2 Relaxation Times 1 Month After ACL Injury

Publication: J Orthop Res. 2022 Jan;40(1):138-49. PMID: 33783030 | PDF

Authors: Wellsandt E, Kallman T, Golightly Y, Podsiadlo D, Dudley A, Vas S, Michaud K, Tao M, Sajja B, Manzer M.

Institution: Division of Physical Therapy Education, University of Nebraska Medical Center, Omaha, NE, USA.

Abstract: Osteoarthritis (OA) is prevalent after anterior cruciate ligament (ACL) injury, but mechanismsunderlying its development are poorly understood. The purpose of this study was to determine if gait biomechanics and daily physical activity (PA) associate with cartilage T2 relaxation times, a marker of collagen organization and water content, 1 month after ACL injury. Twenty-seven participants (15-35 years old) without chondral lesions completed magnetic resonance imaging, three-dimensional gait analysis, and 1 week of PA accelerometry. Interlimb differences and ratios were calculated for gait biomechanics and T2 relaxation times, respectively. Multiple linear regression models adjusted for age, sex, and concomitant meniscus injury were used to determine the association between gait biomechanics and PA with T2 relaxation times, respectively. Altered knee adduction moment (KAM) impulse, less knee flexion excursion (kEXC) and higher daily step counts accounted for 35.8%-65.8% of T2 relaxation time variation in the weightbearing and posterior cartilage of the medial and lateral compartment (all p ≤ .011). KAM impulse was the strongest factor for T2 relaxation times in all models (all p ≤ .001). Lower KAM impulse associated with longer T2 relaxation times in the injured medial compartment (β = -.720 to -.901) and shorter T2 relaxation in the lateral compartment (β = .713 to .956). At 1 month after ACL injury, altered KAM impulse, less kEXC, and higher PA associated with longer T2 relaxation times, which may indicate poorer cartilage health. Statement of Clinical Significance: Gait biomechanics and daily PA are modifiable targets that may improve cartilage health acutely after ACL injury and slow progression to OA.

"Before uninjured segmentation, a manual and affine registration technique was used to register the injured reference images to the uninjured knee using 3D Slicer software."

Low-Dose Lung Radiation Therapy for COVID-19 Lung Disease: A Preclinical Efficacy Study in a Bleomycin Model of Pneumonitis

Publication: Int J Radiat Oncol Biol Phys. 2022 Jan 1;112(1):197-211. PMID: 34478832 | PDF

Authors: Jackson MR, Stevenson K, Chahal SK, Curley E, Finney GE, Gutierrez-Quintana R, Onwubiko E, Rupp A, Strathdee K, Williams K, MacLeod MKL, McSharry C, Chalmers AJ.

Institution: Institute of Cancer Sciences, University of Glasgow, UK.

Abstract: Purpose: Low-dose whole lung radiation therapy (LDLR) has been proposed as a treatment for patients with acute respiratory distress syndrome associated with SARS-CoV-2 infection, and clinical trials are underway. There is an urgent need for preclinical evidence to justify this approach and inform dose, scheduling, and mechanisms of action.

Methods and materials: Female C57BL/6 mice were treated with intranasal bleomycin sulfate (7.5 or 11.25 units/kg, day 0) and then exposed to whole lung radiation therapy (0.5, 1.0, or 1.5 Gy, or sham; day 3). Bodyweight was measured daily, and lung tissue was harvested for histology and flow cytometry on day 10. Computed tomography lung imaging was performed before radiation (day 3) and pre-endpoint (day 10).

Results: Bleomycin caused pneumonitis of variable severity, which correlated with weight loss. LDLR at 1.0 Gy was associated with a significant increase in the proportion of mice recovering to 98% of initial bodyweight, and a proportion of these mice exhibited less severe histopathologic lung changes. Mice experiencing moderate initial weight loss were more likely to respond to LDLR than those experiencing severe initial weight loss. In addition, LDLR (1.0 Gy) significantly reduced bleomycin-induced increases in interstitial macrophages, CD103+ dendritic cells (DCs), and neutrophil-DC hybrids. Overall, bleomycin-treated mice exhibited significantly higher percentages of nonaerated lung in left than right lungs, and LDLR (1.0 Gy) limited further reductions in aerated lung volume in right but not left lungs. LDLR at 0.5 and 1.5 Gy did not improve bodyweight, flow cytometric, or radiologic readouts of bleomycin-induced pneumonitis.

Conclusions: Our data support the concept that LDLR can ameliorate acute inflammatory lung injury, identify 1.0 Gy as the most effective dose, and provide evidence that it is more effective in the context of moderate than severe pneumonitis. Mechanistically, LDLR at 1.0 Gy significantly suppressed bleomycin-induced accumulation of pulmonary interstitial macrophages, CD103+ DCs, and neutrophil-DC hybrids.

"Images were analyzed using the Lung CT analyzer module from the 3D Slicer software extension SlicerCIP."

Knee Cartilage T 2 Relaxation Times 3 Months After ACL Reconstruction Are Associated With Knee Gait Variables Linked to Knee Osteoarthritis

Publication: J Orthop Res. 2022 Jan;40(1):252-9. PMID: 33783867

Authors: Williams JR, Neal K, Alfayyadh A, Lennon K, Capin JJ, Khandha A, Manal K, Potter HG, Snyder-Mackler L, Buchanan TS.

Institution: Department of Mechanical Engineering, University of Delaware, Newark, DE, USA.

Abstract: Osteoarthritis development after ACL reconstruction (ACLR) is not well understood. Investigators have examined associations between knee biomechanical alterations and quantitative MRI (qMRI) variables, reflective of cartilage health, 12-60 months following ACLR; however, none have done so early after surgery. As part of an exploratory study, 45 individuals (age, 23 ± 7 years) underwent motion analysis during walking and qMRI 3 months after ACLR. For each limb, peak knee adduction moment (pKAM) and peak knee flexion moment (pKFM) were determined using inverse dynamics and peak medial compartment force was calculated using a neuromusculoskeletal model. T2 relaxation times in the medial compartment and linear regressions were used to determine the associations between gait variables and deep and superficial cartilage T2 relaxation times in six regions. pKAM was positively associated with deep layer T2 relaxation times within the femoral central and posterior regions when examined in the involved limb and from an interlimb difference perspective (involved limb - uninvolved limb). After adjusting for age, the association between interlimb difference of pKAM and interlimb difference of deep layer T2 relaxation times in the tibial central region became significant (p = .043). Interlimb difference of pKFM was negatively associated with interlimb difference of deep layer T2 relaxation times within the femoral central and posterior regions. These associations suggest that degenerative pathways leading to osteoarthritis may be detectable as early as 3 months after reconstruction. Preventative therapeutic techniques may need to be employed early in the rehabilitation process to prevent cartilage degradation.

"All images were analyzed using the 3D Slicer software."

COVID-19 CT Scan Lung Segmentation: How We Do It

Publication: J Digit Imaging. 2022 Jan 28:1–8. PMID: 35091874 | PDF

Authors: Negroni D, Zagaria D, Paladini A, Falaschi Z, Arcoraci A, Barini M, Carriero A.

Institution: Department of Radiology, "Maggiore Della Carità" Hospital, Novara, Italy.

Abstract: The National Health Systems have been severely stressed out by the COVID-19 pandemic because 14% of patients require hospitalization and oxygen support, and 5% require admission to an Intensive Care Unit (ICU). Relationship between COVID-19 prognosis and the extent of alterations on chest CT obtained by both visual and software-based quantification that expresses objective evaluations of the percentage of ventilated lung parenchyma compared to the affected one has been proven. While commercial applications for automatic medical image computing and visualization are expensive and limited in their spread, the open-source systems are characterized by not enough standardization and time-consuming troubles. We analyzed chest CT exams on 246 patients suspected of COVID-19 performed in the Emergency Department CT room. The lung parenchyma segmentation was obtained by a threshold-based method using the open-source 3D Slicer software and software tools called "Segment Editor" and "Segment Quantification." For the three main characteristics analyzed on lungs affected by COVID-19 pneumonia, a specifical densitometry value range was defined: from - 950 to - 700 HU for well-aerated parenchyma; from - 700 to - 250 HU for interstitial lung disease; from - 250 to 250 HU for parenchymal consolidation. For the well-aerated parenchyma and the interstitial alterations, the procedure was semi-automatic with low time consumption, whereas consolidations' analysis needed manual interventions by the operator. After the chest CT, 13% of the sample was admitted to intensive care, while 34% of them to the sub-intensive care. In patients moved to intensive care, the parenchyma analysis reported a higher crazy paving presentation. The quantitative analysis of the alterations affecting the lung parenchyma of patients with COVID-19 pneumonia can be performed by threshold method segmentation on 3D Slicer. The segmentation could have an important role in the quantification in different COVID-19 pneumonia presentations, allowing to help the clinician in the correct management of patients.

Prognostic Value of Tumor Measurement Parameters and SCC-Ag Changes in Patients With Locally-Advanced Cervical Cancer

Publication: Radiat Oncol. 2022 Jan 10;17(1):6. PMID: 35012582 | PDF

Authors: Chen W, Xiu S, Xie X, Guo H, Xu Y, Bai P, Xia X.

Institution: Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fujian, China.

Abstract: Objective: To investigate the prognostic relevance of specific measurement parameters such as tumor diameter, tumor volume, tumor volume reduction rate (TVRR), and changes in the squamous cell carcinoma antigen (SCC-Ag) level in patients with locally-advanced cervical cancer (LACC) undergoing concurrent radiotherapy and chemotherapy.

Methods: This was a retrospective study of 203 patients with stage IIA-IVA cervical squamous cell carcinoma who were newly diagnosed at our hospital between January 2011 and March 2015. Clinical data and pre-and post-treatment imaging information were collected and each parameter was calculated using 3D Slicer software. The pre/post-treatment tumor diameter (TDpre/post), tumor volume (TVpre/post), SCC-Ag (SCCpre/post), and TVRR, SCC-Ag reduction rate (SCCRR) were analyzed and their prognostic relevance evaluated.

Results: The median follow-up was 69 months. The 5-year overall survival (OS) and disease progression-free survival (PFS) rates were 69.5% and 64.5%, respectively. On univariate analysis, TDpre/post, TVpre/post, TVRR, SCCpre/post and SCCRR showed significant association with OS and PFS (P < 0.05). On multivariate analysis, TDpre [Hazard ratio (HR) = 0.373, P = 0.028], TDpost (HR = 0.376, P = 0.003) and SCCpost (HR = 0.374, P = 0.001) were independent predictors of OS. TVRR (HR = 2.998, P < 0.001), SCCpre (HR = 0.563, P = 0.041), and SCCpost (HR = 0.253, P < 0.001) were independent predictors of PFS. Tumor measurement parameters showed a positive correlation with SCC-Ag (P < 0.05).

Conclusion: TDpre/post, TVpre/post, TVRR, SCCpre/post, and SCCRR were prognostic factors in LACC. TDpre/post and SCCpost showed the most significant prognostic value. TVRR and SCCpre/post were closely related to disease progression. Further studies should investigate the correlation between measurement parameters of tumor and SCC-Ag.

MRI Radiomic Features-Based Machine Learning Approach to Classify Ischemic Stroke Onset Time

Publication: J Neurol. 2022 Jan;269(1):350-60. PMID: 34218292

Authors: Zhang YQ, Liu AF, Man FY, Zhang YY, Li C, Liu YE, Zhou J, Zhang AP, Zhang YD, Lv J, Jiang WJ.

Institution: Department of Vascular Neurosurgery, New Era Stroke Care and Research Institute, The PLA Rocket Force Characteristic Medical Center, Beijing, China.

Abstract: Purpose: We aimed to investigate the ability of MRI radiomics features-based machine learning (ML) models to classify the time since stroke onset (TSS), which could aid in stroke assessment and treatment options.

Methods: This study involved 84 patients with acute ischemic stroke due to anterior circulation artery occlusion (51 in the training cohort and 33 in the independent test cohort). Region of infarct segmentation was manually outlined by 3D Slicer software. Image processing including registration, normalization and radiomics features calculation were done in R (version 3.6.1). A total of 4312 radiomic features from each image sequence were captured and used in six ML models to estimate stroke onset time for binary classification (≤ 4.5 h). Receiver-operating characteristic curve (ROC) and other parameters were calculated to evaluate the performance of the models in both training and test cohorts.

Results: Twelve radiomics and six clinic features were selected to construct the ML models for TSS classification. The deep learning model-based DWI/ADC radiomic features performed the best for binary TSS classification in the independent test cohort, with an AUC of 0.754, accuracy of 0.788, sensitivity of 0.952, specificity of 0.500, positive predictive value of 0.769, and negative predictive value of 0.857, respectively. Furthermore, adding clinical information did not improve the performance of the DWI/ADC-based deep learning model. The TSS prediction models can be visited at: .

Conclusions: A unique deep learning model based on DWI/ADC radiomic features was constructed for TSS classification, which could aid in decision making for thrombolysis in patients with unknown stroke onset.

Translation and Rotation Analysis Based on Stress MRI for the Diagnosis of Anterior Cruciate Ligament Tears

Publication: Quant Imaging Med Surg. 2022 Jan; 12(1): 257–68. PMID: 34993076 | PDF

Authors: Klon W, Domżalski M, Malinowski K,Sadlik B

Institution: St Luke’s Hospital, Bielsko-Biała, Poland.

Abstract: Due to the increasing need for a detailed biomechanical analysis of anterior cruciate ligament (ACL) lesions, the aim of the study was to develop a method of direct measurement of the three-dimensional tibial translation and rotation based on stress MRI.

Methods For the purpose of the study, thirty patients with acute ACL rupture and 17 healthy control subjects were selected. Based on clinical examination, they were qualified for MRI examination using the Arthroholder Device prototype to perform anterior tibial translation. Each examination was performed at 30° of knee flexion, initially without tibia translation and then using the force applied to the calf of 80 N. The femur and tibia were separately registered using rigid local SimpleITK landmark refinement; translation and rotation parameters were then calculated using the 3D transformation algorithms. The significance level was set at 0.05.

Results Initially, the device and method for obtaining the parameters of the 3D translation and rotation were validated. The pooled Standard Deviation for translation parameters was 0.81 mm and for rotation parameters 0.87°. Compared to the control group, statistically significant differences were found in parameters such as Anterior Shift [(median ± interquartile range) 3.89 mm ±6.55 vs. 0.90 mm ±2.78, P=0.002238] and External Rotation (−0.55° ±3.88 vs. −2.87° ±2.40, P=0.005074). Statistically significant correlations were observed in combined groups between Anterior Shift and parameters such as External Rotation (P=0.001611), PCL Tibial Attachment Point (pPCL) Anterior Shift (<0.000001), Rolimeter Measurement (P=0.000016), and Side-to-Side Difference (SSD) (P=0.000383). A significant statistical correlation was also observed between External Rotation and parameters such as Rolimeter (P=0.02261) and SSD (P=0.03458).

Conclusions The analysis of the anterior tibia translation using stress MRI and the proposed three-dimensional calculation method allows for a detailed analysis of the tibial translation and rotation parameters. The correlations showed the importance of external rotation during anterior tibial translation.

The Relationship of LDH and Hematological Parameters with Ischemic Volume and Prognosis in Cerebrovascular Disease

Publication: J Coll Physicians Surg Pak. 2022 Jan;32(1):42-45. PMID: 34983146

Authors: Alatlı T, Kocaoglu S, Akay E.

Institution: Department of Emergency, Faculty of Medicine, Balikesir University, Balikesir, Turkey.

Abstract: Objective: To determine whether lactate dehydrogenase (LDH), platelet-lymphocyte ratio (PLR), neutrophil-lymphocyte ratio (NLR), and lymphocyte-monocyte ratio (LMR) values can be used as a prediction for their relationship with stroke volume (SV) and for in-hospital mortality in stroke patients in Emergency Department (ED).

Study design: Analytical study.

Place and duration of study: Balikesir University, Turkey from 24/03/2021 to 30/06/2021.

Methodology: Patients aged 18 years or older, diagnosed with stroke in ED, were included in the study. Stroke volumes were calculated from diffusion-weighted images (DWi) with 3D Slicer software using image-based semi-automatic and manual segmentation methods.

Results: Of the 265 patients, 128 (48.3%) were males. SV was significantly higher in the non-survivor group than in the survivor group (p=0.007). NLR was significantly higher in the non-survivor group than in the survivor group (p=0.018).

Conclusion: The ratios of NLR and SV stand out as practical parameters for the estimation of mortality, prognosis, and management of patients diagnosed with acute stroke. Taking into account, these parameters in the diagnosis process and prognosis management in EDs will provide convenience.