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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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Artificial intelligence reveals brain aging patterns in 27,402 individuals without diagnosed cognitive impairment that are linked to genetics, biomedical measures, and cognitive decline

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Alzheimer's & Dementia 2023年第S17期19卷

作者： Ioanna Skampardoni Ilya M. Nasrallah Junhao Wen Yuhan Cui Ahmed Abdulkadir Zhijian Yang Guray Erus Elizabeth Mamourian Ashish Singh Haochang Shou Li Shen Konstantina Nikita Christos Davatzikos iSTAGING consortium School of Electrical and Computer Engineering National Technical University of Athens Athens Greece Centre for Biomedical Image Computing and Analytics University of Pennsylvania Philadelphia PA USA Correspondece Department of Radiology University of Pennsylvania Philadelphia PA USA Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL) Center for and Data Science for Integrated Diagnostics (AI2D) Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL) Center for and Data Science for Integrated Diagnostics (AI2D) Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Laboratory for Research in Neuroimaging Department of Clinical Neurosciences Lausanne University Hospital (CHUV) and University of Lausanne Lausanne Switzerland 1Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL) Center for and Data Science for Integrated Diagnostics (AI2D) Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Biostatistics Epidemiology & Informatics University of Pennsylvania Philadelphia PA USA University of Pennsylvania Philadelphia PA USA

Background Understanding heterogeneity of structural brain changes in aging may provide insights into susceptibility to neurodegenerative diseases. We characterize the genetics underlying brain structural heterogeneity within cognitively unimpaired (CU) individuals using data-driven machine learning applied to a diverse dataset of 27,402 individuals from 11 neuroimaging studies from the iSTAGING consortium. Method Structural brain morphologic patterns of CU individuals were independently examined in four decade-long intervals spanning ages 45 to 85. Within each interval, Smile-GAN (Yang et al., 2021) was trained on baseline anatomic and white matter hyperintensity (WMH) volumes. Smile-GAN probability scores were used as phenotypes in genome-wide association studies (GWAS). Specifically, we performed multiple linear regressions controlling for confounders (e.g., age) via Plink (Purcell et al., 2007). We observed longitudinal clustering stability across decades, so individuals from adjacent age groups were combined into broader age groups ([45,65), [65,85)) due to the large sample requirement of GWAS. Genomic loci, represented by the top leading single nucleotide polymorphisms (SNPs), were defined considering linkage disequilibrium. We investigated associations of SNPs with clinical traits and mapped them to genes using the GWAS Catalog (Buniello et al., 2019). Result Three structural brain aging patterns, relative to resilient agers (A0), consistent across decades, emerged: A1, or ‘typical’ aging with low atrophy and WMHs, and two ‘advanced’ aging patterns, one showing elevated WMHs and modest atrophy (A2) and the other displaying severe, widespread atrophy and moderate WMH load (A3) (Figure 1). GWAS discovered eight and six genomic loci in [45,65) and [65,85) age groups, respectively (Table 1, Figure 2). The lead SNPs for A1 and A2 were previously associated with several cardiometabolic risk factors, WMHs, and regional brain volumes. Interestingly, rs4843552, previo

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Multidimensional representations in late-life depression: Convergence in neuroimaging, cognition, clinical symptomatology and genetics

arXiv

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arXiv 2021年

作者： Wen, Junhao Fu, Cynthia H.Y. Tosun, Duygu Veturi, Yogasudha Yang, Zhijian Abdulkadir, Ahmed Mamourian, Elizabeth Srinivasan, Dhivya Bao, Jingxuan Erus, Guray Shou, Haochang Habes, Mohamad Doshi, Jimit Varol, Erdem Mackin, Scott R. Sotiras, Aristeidis Fan, Yong Saykin, Andrew J. Sheline, Yvette I. Shen, Li Ritchie, Marylyn D. Wolk, David A. Albert, Marilyn Resnick, Susan M. Davatzikos, Christos Center for Biomedical Image Computing and Analytics Perelman School of Medicine University of Pennsylvania Philadelphia United States University of East London School of Psychology London United Kingdom Centre for Affective Disorders Institute of Psychiatry Psychology and Neuroscience King’s College London London United Kingdom Department of Radiology and Biomedical Imaging University of California San FranciscoCA United States Department of Genetics Institute for Biomedical Informatics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Perelman School of Medicine PhiladelphiaPA19104 United States Penn Statistics in Imaging and Visualization Center Department of Biostatistics Epidemiology and Informatics Perelman School of Medicine University of Pennsylvania Philadelphia United States Glenn Biggs Institute for Alzheimer’s & Neurodegenerative Diseases University of Texas Health Science Center at San Antonio San Antonio United States Department of Statistics Center for Theoretical Neuroscience Zuckerman Institute Columbia University New York United States Department of Psychiatry University of California San FranciscoCA United States Department of Radiology Institute for Informatics Washington University School of Medicine St. Louis United States Radiology and Imaging Sciences Center for Neuroimaging Department of Radiology and Imaging Sciences Indiana Alzheimer’s Disease Research Center Melvin and Bren Simon Cancer Center Indiana University School of Medicine Indianapolis United States Center for Neuromodulation in Depression and Stress Department of Psychiatry University of Pennsylvania Perelman School of Medicine PhiladelphiaPA United States Department of Neurology Penn Memory Center University of Pennsylvania Philadelphia United States Department of Neurology Johns Hopkins University School of Medicine United States Laboratory o

Importance: Late-life depression (LLD) is characterized by considerable heterogeneity in clinical manifestation. Unraveling such heterogeneity would aid in elucidating etiological mechanisms and pave the road to precision and individualized medicine. Objective: We sought to delineate, cross-sectionally and longitudinally, disease-related heterogeneity in LLD linked to neuroanatomy, cognitive functioning, clinical symptomatology, and genetic profiles. Design & setting: The iSTAGING study is an international multicenter consortium investigating brain aging in pooled and harmonized data from 13 studies with over 35,000 participants, including a subset of individuals with major depressive disorders. Participants: Multimodal data from a multicentre sample (N=996), including neuroimaging, neurocognitive assessments, and genetics: 501 LLD participants (332 women, mean age 67.39 ± 5.56 years) and 495 healthy controls (333 women, mean age 66.53 ± 5.16 years) were analyzed. A semi-supervised clustering method (HYDRA) was applied to regional grey matter (GM) brain volumes to derive dimensional representations. Exposure: None Main outcome and Measure: Two dimensions were identified, which accounted for the LLD-related heterogeneity in voxel-wise GM maps, white matter (WM) fractional anisotropy (FA), neurocognitive functioning, clinical phenotype, and genetics. Results: Dimension one (Dim1) demonstrated relatively preserved brain anatomy without WM disruptions relative to healthy controls. In contrast, dimension two (Dim2) showed widespread brain atrophy and WM integrity disruptions, along with cognitive impairment and higher depression severity. Moreover, one de novo independent genetic variant (rs13120336) was significantly associated with Dim 1 but not with Dim 2. Notably, the two dimensions demonstrated significant SNP-based heritability of 18-27% within the general population (N=12,518 in UKBB). Lastly, in a subset of individuals having longitudinal measurements, Dim2 demon

关键词： Neuroimaging

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NIMG-33. PROGNOSTIC STRATIFICATION OF DE NOVO GLIOBLASTOMA PATIENTS ACROSS 22 GEOGRAPHICALLY DISTINCT INSTITUTIONS: UPDATES FROM THE RESPOND CONSORTIUM

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Neuro-Oncology 2022年第SUPPLEMENT_7期24卷 vii170–vii170页

作者： Akbari, Hamed Bakas, Spyridon Sako, Chiharu Kazerooni, Anahita Fathi Villanueva-Meyer, Javier Garcia, Jose Bagley, Stephen Baid, Ujjwal Bilello, Michel Brem, Steven Lustig, Robert Mohan, Suyash Nasrallah, MacLean O'Rourke, Donald Calabrese, Evan Rudie, Jeffrey LaMontagne, Pamela Marcus, Daniel Balana, Carmen Capellades, Jaume Puig, Josep Barnholtz-Sloan, Jill Badve, Chaitra Sloan, Andrew Ak, Murat Colen, Rivka Ahn, Sung Soo Chang, Jong Hee Choi, Yoon Seong Lee, Seung-Koo Dicker, Adam Flanders, Adam Shi, Wenyin Shukla, Gaurav Griffith, Brent Poisson, Laila Rogers, Lisa Booth, Thomas Jain, Rajan Lee, Matthew Mahajan, Abhishek Chakravarti, Arnab Palmer, Joshua Taylor, William Cepeda, Santiago Wiestler, Benedikt Davatzikos, Christos University of Pennsylvania Philadelphia PA USA Center for Biomedical Image Computing and Analytics Department of Radiology and Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Center for Biomedical Image Computing and Analytics and Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia USA University of Pennsylvania Philadelphia USA University of California San Francisco San Francisco CA USA Hospital of the University of Pennsylvania Philadelphia PA USA Hospital of the University of Pennsylvania Philadelphia USA Center for Biomedical Image Computing and Analytics Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA University of California San Francisco San Francisco USA Washington University School of Medicine St. Louis USA Department of Radiology Washington University School of Medicine St. Louis MO USA Medical Oncology Department Catalan Institute of Oncology Barcelona Spain Department of Medical Imaging Consorci MAR Parc de Salut Barcelona Spain Department of Radiology (IDI) and Girona Biomedical Research Institute (IDIBGI) Hospital Universitari de Girona Dr Josep Trueta Girona Spain Center for Biomedical Informatics and Information Technology and Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA Department of Radiology Case Western Reserve University and University Hospitals Cleveland Medical Center Cleveland USA Department of Pathology and Department of Neurosurgery Case Western Reserve University and University Hospitals Cleveland Medical Center Seidman Cancer Center and Case Comprehensive Cancer Center Cleveland USA University of Pittsburgh Pittsburgh USA Department of Radiology University of Pittsburgh Pittsburgh PA USA Yons

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NIMG-67. MULTI-PARAMETRIC MRI-BASED MACHINE LEARNING ANALYSIS FOR PREDICTION OF NEOPLASTIC INFILTRATION AND RECURRENCE IN PATIENTS WITH GLIOBLASTOMA: UPDATES FROM THE MULTI-INSTITUTIONAL RESPOND CONSORTIUM

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Neuro-Oncology 2022年第SUPPLEMENT_7期24卷 vii179–vii180页

作者： Akbari, Hamed Mohan, Suyash Garcia, Jose Kazerooni, Anahita Fathi Sako, Chiharu Bakas, Spyridon Bilello, Michel Bagley, Stephen Baid, Ujjwal Brem, Steven Lustig, Robert Nasrallah, MacLean O'Rourke, Donald Barnholtz-Sloan, Jill Badve, Chaitra Sloan, Andrew Jain, Rajan Lee, Matthew Chakravarti, Arnab Palmer, Joshua Taylor, William Cepeda, Santiago Dicker, Adam Flanders, Adam Shi, Wenyin Shukla, Gaurav Calabrese, Evan Rudie, Jeffrey Villanueva-Meyer, Javier LaMontagne, Pamela Marcus, Daniel Balana, Carmen Capellades, Jaume Puig, Josep Ak, Murat Colen, Rivka Ahn, Sung Soo Chang, Jong Hee Choi, Yoon Seong Lee, Seung-Koo Griffith, Brent Poisson, Laila Rogers, Lisa Booth, Thomas Mahajan, Abhishek Wiestler, Benedikt Davatzikos, Christos University of Pennsylvania Philadelphia PA USA Center for Biomedical Image Computing and Analytics Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA University of Pennsylvania Philadelphia USA Center for Biomedical Image Computing and Analytics and Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia USA Center for Biomedical Image Computing and Analytics Department of Radiology and Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Hospital of the University of Pennsylvania Philadelphia PA USA Hospital of the University of Pennsylvania Philadelphia USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Center for Biomedical Informatics and Information Technology and Division of Cancer Epidemiology and Genetics National Cancer Institute Bethesda MD USA Department of Radiology Case Western Reserve University and University Hospitals Cleveland Medical Center Cleveland USA Department of Pathology and Department of Neurosurgery Case Western Reserve University and University Hospitals Cleveland Medical Center Seidman Cancer Center and Case Comprehensive Cancer Center Cleveland USA Department of Radiology NYU Grossman School of Medicine New York NY USA Department of Radiation Oncology Ohio State University Wexner Medical Center Columbus OH USA The Department of Radiation Oncology The James Cancer Hospital Ohio State University Wexner Medical Center Columbus OH USA The Ohio State University Columbus USA University Hospital Río Hortega Valladolid Spain Department of Radiation Oncology Sidney Kimmel Cancer Center Thomas Jefferson University Philadelphia PA USA Department of Radiology Sidney Kimmel Cancer Center Thomas Jefferson University Philadelphia PA USA Department of Radiation Oncology Thomas Jefferson University Hospita

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Out-of-the box automated computation of cortical thickness of the medial perirhinal cortex does not replace segmentation by hand

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Alzheimer's & Dementia 2023年第S17期19卷

作者： Nicolas A. Henzen Ahmed Abdulkadir Julia Reinhardt Maria Blatow Reto W. Kressig Sabine Krumm University Department of Geriatric Medicine FELIX PLATTER Basel Switzerland Faculty of Psychology University of Basel Basel Switzerland Correspondece Laboratory for Research in Neuroimaging Department of Clinical Neurosciences Lausanne University Hospital (CHUV) and University of Lausanne Lausanne Switzerland Centre for Biomedical Image Computing and Analytics University of Pennsylvania Philadelphia PA USA Division of Diagnostic and Interventional Neuroradiology University Hospital Basel University of Basel Basel Switzerland Department of Cardiology and Cardiovascular Research Institute Basel (CRIB) University Hospital Basel University of Basel Switzerland Basel Switzerland Department of Orthopedic Surgery and Traumatology University Hospital of Basel University of Basel Basel Switzerland Basel Switzerland Section of Neuroradiology Department of Radiology and Nuclear Medicine Neurocenter Cantonal Hospital Lucerne University of Lucerne Lucerne Switzerland Lucerne Switzerland Faculty of Medicine University of Basel Basel Switzerland

Background Cortical thickness of the medial perirhinal cortex (mPRC) is a promising marker of early, potentially pre-clinical Alzheimer’s disease (AD) because atrophy of this region is causally linked to intracellular neurofibrillary tangles. Neurofibrillary pathology, a major neuropathological characteristic of AD, typically starts in the mPRC, also referred to as the transentorhinal cortex. From there it spreads to the entorhinal cortex and eventually to the hippocampus. To date, no tools exist that automatically compute the cortical thickness of the mPRC, most likely because of the novelty and complexity of the manual segmentation protocol and the large variability of the morphology of the mPRC. Herein, we aimed to develop an automated segmentation algorithm for the mPRC. Method An experienced rater (SK) manually segmented the mPRC from two data sets (train: n = 103; test: n = 44) using the FreeSurfer segmentation tools. The train data set (mean age = 76.4 ± 7.0 years; normal controls and patients with AD) was used to train the native FreeSurfer segmentation algorithm with the custom region as well as a voxel-based deep convolutional neural network based on nnUNet with minimal adaptations to the training protocol. In a next step, the trained models were applied to the test data set (mean age = 69.2 ± 10.4 years; normal controls, AD, major depression, and mild cognitive impairment or dementia due to other etiologies than AD) and cortical thickness values were extracted. Finally, cortical thickness values of both segmentations were compared individually to the manual segmentation. Results Intraclass correlation coefficients (ICCs) between FreeSurfer and the manual segmentation reached .768 for the left hemisphere (lh) and .835 for the right hemisphere (rh). The deep learning method compared to the manual segmentation achieved ICCs of .840 for lh and .896 for rh. Conclusion The deep learning based procedure outperformed the native FreeSurfer segmentation in this com

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A large-scale ENIGMA multisite replication study of brain age in depression

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Neuroimage: Reports 2022年第4期2卷 100149-100149页

作者： Han, Laura K.M. Dinga, Richard Leenings, Ramona Hahn, Tim Cole, James H. Aftanas, Lyubomir I. Amod, Alyssa R. Besteher, Bianca Colle, Romain Corruble, Emmanuelle Couvy-Duchesne, Baptiste Danilenko, Konstantin V. Fuentes-Claramonte, Paola Gonul, Ali Saffet Gotlib, Ian H. Goya-Maldonado, Roberto Groenewold, Nynke A. Hamilton, Paul Ichikawa, Naho Ipser, Jonathan C. Itai, Eri Koopowitz, Sheri-Michelle Li, Meng Okada, Go Okamoto, Yasumasa Churikova, Olga S. Osipov, Evgeny A. Penninx, Brenda W.J.H. Pomarol-Clotet, Edith Rodríguez-Cano, Elena Sacchet, Matthew D. Shinzato, Hotaka Sim, Kang Stein, Dan J. Uyar-Demir, Aslihan Veltman, Dick J. Schmaal, Lianne Centre for Youth Mental Health The University of Melbourne Parkville VIC Australia Orygen Parkville VIC Australia Department of Cognitive Science & Artificial Intelligence Tilburg University Tilburg Netherlands Institute for Translational Psychiatry University of Münster Münster Germany Faculty of Mathematics and Computer Science University of Münster Münster Germany Centre for Medical Image Computing Department of Computer Science University College London United Kingdom Dementia Research Centre Queen Square Institute of Neurology University College London United Kingdom Scientific Research Institute of Neuroscience and Medicine Novosibirsk Russian Federation Novosibirsk State University Novosibirsk Russian Federation Department of Psychiatry & Mental Health Neuroscience Institute University of Cape Town South Africa Department of Psychiatry and Psychotherapy Jena University Hospital Jena Germany Service Hospitalo-Universitaire de Psychiatrie de Bicêtre Mood Center Paris Saclay Assistance Publique-Hôpitaux de Paris Hôpitaux Universitaires Paris-Saclay Hôpital de Bicêtre Le Kremlin Bicêtre F-94275 France MOODS Team INSERM 1018 CESP (Centre de Recherche en Epidémiologie et Santé des Populations) Université Paris-Saclay Faculté de Médecine Paris-Saclay Le Kremlin Bicêtre F-94275 France Sorbonne Université Institut du Cerveau - Paris Brain Institute - ICM CNRS Inria Inserm AP-HP Hôpital de La Pitié Salpêtrière Paris F-75013 France Institute for Molecular Bioscience The University of Queensland St Lucia 4072 QLD Australia FIDMAG Hermanas Hospitalarias Research Foundation Barcelona Spain CIBERSAM Barcelona Spain SoCAT Lab Department of Psychiatry School of Medicine Ege University Izmir Turkey Department of Psychology Stanford University Stanford CA United States Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab) University Medical Center Göttingen Göttingen Germany Center for Social and Affective Neuroscience Department o

Background: Several studies have evaluated whether depressed persons have older appearing brains than their nondepressed peers. However, the estimated neuroimaging-derived “brain age gap” has varied from study to study, likely driven by differences in training and testing sample (size), age range, and used modality/features. To validate our previously developed ENIGMA brain age model and the identified brain age gap, we aim to replicate the presence and effect size estimate previously found in the largest study in depression to date (N = 2126 controls & N = 2675 cases;+1.08 years [SE 0.22], Cohen's d = 0.14, 95% CI: 0.08–0.20), in independent cohorts that were not part of the original study. Methods: A previously trained brain age model (***/enigma_brainage) based on 77 FreeSurfer brain regions of interest was used to obtain unbiased brain age predictions in 751 controls and 766 persons with depression (18–75 years) from 13 new cohorts collected from 20 different scanners. Meta-regressions were used to examine potential moderating effects of basic cohort characteristics (e.g., clinical and scan technical) on the brain age gap. Results: Our ENIGMA MDD brain age model generalized reasonably well to controls from the new cohorts (predicted age vs. age: r = 0.73, R² = 0.47, MAE = 7.50 years), although the performance varied from cohort to cohort. In these new cohorts, on average, depressed persons showed a significantly higher brain age gap of +1 year (SE 0.35) (Cohen's d = 0.15, 95% CI: 0.05–0.25) compared with controls, highly similar to our previous finding. Significant moderating effects of FreeSurfer version 6.0 (d = 0.41, p = 0.007) and Philips scanner vendor (d = 0.50, p < 0.0001) were found, leading to more positive effect size estimates. Conclusions: This study further validates our previously developed ENIGMA brain age algorithm. Importantly, we replicated the brain age gap in depression with a comparable effect size. Thus, two large-s

关键词： Biological aging Brain age Depression ENIGMA consortium Replication study

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A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

arXiv

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arXiv 2024年

作者： de la Rosa, Ezequiel Reyes, Mauricio Liew, Sook-Lei Hutton, Alexandre Wiest, Roland Kaesmacher, Johannes Hanning, Uta Hakim, Arsany Zubal, Richard Valenzuela, Waldo Robben, David Sima, Diana M. Anania, Vincenzo Brys, Arne Meakin, James A. Mickan, Anne Broocks, Gabriel Heitkamp, Christian Gao, Shengbo Liang, Kongming Zhang, Ziji Siddiquee, Md Mahfuzur Rahman Myronenko, Andriy Ashtari, Pooya Van Huffel, Sabine Jeong, Hyun-Su Yoon, Chi-Ho Kim, Chulhong Huo, Jiayu Ourselin, Sebastien Sparks, Rachel Clèrigues, Albert Oliver, Arnau Lladó, Xavier Chalcroft, Liam Pappas, Ioannis Bertels, Jeroen Heylen, Ewout Moreau, Juliette Hatami, Nima Frindel, Carole Qayyum, Abdul Mazher, Moona Puig, Domenec Lin, Shao-Chieh Juan, Chun-Jung Hu, Tianxi Boone, Lyndon Goubran, Maged Liu, Yi-Jui Wegener, Susanne Kofler, Florian Ezhov, Ivan Shit, Suprosanna Hernandez Petzsche, Moritz R. Menze, Bjoern Kirschke, Jan S. Wiestler, Benedikt Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Informatics Technical University Munich Germany Icometrix Leuven Belgium ARTORG Center for Biomedical Research University of Bern Bern Switzerland Department of Radiation Oncology University Hospital Bern University of Bern Switzerland University of Bern Bern Switzerland Chan Division of Occupational Science and Occupational Therapy University of Southern California Los AngelesCA United States Stevens Neuroimaging and Informatics Institute Department of Neurology Keck School of Medicine University of Southern California United States University Institute of Diagnostic and Interventional Neuroradiology Inselspital Bern Switzerland University Institute of Diagnostic and Interventional Neuroradiology University Hospital Bern Inselspital University of Bern Bern Switzerland Department of Diagnostic and Interventional neuroradiology University Medical Center Hamburg-Eppendorf Hamburg Germany Department of Medical Imaging Radboud University Medical Center Institute for Health Sciences Nijmegen Netherlands Deepwise AI Lab Beijing China Beijing University of Posts and Telecommunications Bejing China School of Computing and Augmented Intelligence Arizona State University TempeAZ United States NVIDIA Santa ClaraCA United States STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Pohang Korea Republic of School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Institute of Computer Vision and Robotics University of Girona Spain Wellcome Centre for Human Neuroimaging University College London London United Kingdom Laboratory of Neuro Imaging Stevens Institute for Neuroimaging and Informatics Keck School of Medicine University of Southern California Los Angeles United States KU Leuven Leuven Belgium CREATIS Université Lyon1 CNRS UMR5220 INSERM U1206 INSA-Lyon Villeurbanne696

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES’22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. By assessing them against a hidden test set, we identified strengths, weaknesses, and potential biases. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model combines the individual algorithms’ strengths and achieved superior ischemic lesion detection and segmentation accuracy (median Dice score: 0.82, median lesion-wise F1 score: 0.86) on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers like lesion types and affected vascular territories. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm’s segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model’s generalizability (median Dice score: 0.82, median lesion-wise F1 score: 0.86). The algorithm’s outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)rad

关键词： Diagnosis

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Paired plasma lipidomics and proteomics analysis in the conversion from mild cognitive impairment to Alzheimer's disease

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Computers in Biology and Medicine 2024年 176卷 108588-108588页

作者： Gómez-Pascual, Alicia Naccache, Talel Xu, Jin Hooshmand, Kourosh Wretlind, Asger Gabrielli, Martina Lombardo, Marta Tiffany Shi, Liu Buckley, Noel J. Tijms, Betty M. Vos, Stephanie J.B. ten Kate, Mara Engelborghs, Sebastiaan Sleegers, Kristel Frisoni, Giovanni B. Wallin, Anders Lleó, Alberto Popp, Julius Martinez-Lage, Pablo Streffer, Johannes Barkhof, Frederik Zetterberg, Henrik Visser, Pieter Jelle Lovestone, Simon Bertram, Lars Nevado-Holgado, Alejo J. Gualerzi, Alice Picciolini, Silvia Proitsi, Petroula Verderio, Claudia Botía, Juan A. Legido-Quigley, Cristina Department of Information and Communications Engineering Faculty of Informatics University of Murcia Murcia Spain Steno Diabetes Center Copenhagen Herlev Denmark Department of Data Science City University of London United Kingdom Institute of Pharmaceutical Science King's College London London United Kingdom CNR Institute of Neuroscience Vedano al Lambro20854 Italy School of Medicine and Surgery University of Milano-Bicocca 20126 Italy Oxford United Kingdom Department of Psychiatry University of Oxford United Kingdom Kavli Institute for Nanoscience Discovery Denmark Alzheimer Center VU University Medical Center Amsterdam Netherlands Department of Psychiatry and Neuropsychology Alzheimer Centrum Limburg Maastricht University Maastricht Netherlands Department of Biomedical Sciences University of Antwerp Antwerp Belgium Vrije Universiteit Brussel Brussels Belgium Complex Genetics Group VIB Center for Molecular Neurology VIB Antwerp Belgium Institute Born-Bunge Department of Biomedical Sciences University of Antwerp Antwerp Belgium University of Geneva Geneva Switzerland IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy Institute of Neuroscience and Physiology Sahlgrenska Academy at University of Gothenburg Gothenburg Sweden Barcelona Spain Old age psychiatry University Hospital of Lausanne University of Lausanne Switzerland Department of Geriatric Psychiatry University Hospital of Psychiatry Zürich University of Zürich Switzerland CITA-Alzheimer Foundation San Sebastian Spain AC Immune SA formerly Janssen R&D LLC. Beerse Belgium at the time of study conduct Lausanne Switzerland Department of Radiology and Nuclear Medicine Amsterdam UMC Vrije Universiteit Netherlands Queen Square Institute of Neurology and Centre for Medical Image Computing University College London United Kingdom Clinical Neurochemistry Laboratory Sahlgrenska University Hospital Mölndal Sweden Department of Psychiatry and Neurochemistry Institute of

Background: Alzheimer's disease (AD) is a neurodegenerative condition for which there is currently no available medication that can stop its progression. Previous studies suggest that mild cognitive impairment (MCI) is a phase that precedes the disease. Therefore, a better understanding of the molecular mechanisms behind MCI conversion to AD is needed. Method: Here, we propose a machine learning-based approach to detect the key metabolites and proteins involved in MCI progression to AD using data from the European Medical Information Framework for Alzheimer's Disease Multimodal Biomarker Discovery Study. Proteins and metabolites were evaluated separately in multiclass models (controls, MCI and AD) and together in MCI conversion models (MCI stable vs converter). Only features selected as relevant by 3/4 algorithms proposed were kept for downstream analysis. Results: Multiclass models of metabolites highlighted nine features further validated in an independent cohort (0.726 mean balanced accuracy). Among these features, one metabolite, oleamide, was selected by all the algorithms. Further in-vitro experiments in rodents showed that disease-associated microglia excreted oleamide in vesicles. Multiclass models of proteins stood out with nine features, validated in an independent cohort (0.720 mean balanced accuracy). However, none of the proteins was selected by all the algorithms. Besides, to distinguish between MCI stable and converters, 14 key features were selected (0.872 AUC), including tTau, alpha-synuclein (SNCA), junctophilin-3 (JPH3), properdin (CFP) and peptidase inhibitor 15 (PI15) among others. Conclusions: This omics integration approach highlighted a set of molecules associated with MCI conversion important in neuronal and glia inflammation pathways. © 2024 The Authors

关键词： Metabolites

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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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