Main Page/SlicerCommunity/2022

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

• 1,467,466+ downloads in the last 11 years (269,677 in 2023, 206,541 in 2022)
• over 17.900+ literature search results on Google Scholar
  • 13,400+ cancer
  • 7.290+ brain
  • 6,380+ lung
  • 3,980+ breast
  • 3,080+ prostate

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

• 39 events in open source hackathon series continuously running since 2005 with 3260 total participants
• Slicer Forum with +8,138 subscribers has approximately 275 posts every week

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

2022

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.

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: Durongbhan P, Davey CE, Stok KS. 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.

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 Jan 21. 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.

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.

3D Visualization of Perianal Fistulas Using Parametric Models

Publication: Tech Coloproctol. 2022 Jan 30. 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.

3D Slicer

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: 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.

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: http://123.57.65.199:3838/deeptss/ . 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.