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THE DEVELOPMENT OF A HARMONIZED SEGMENTATION PROTOCOL FOR HIPPOCAMPAL SUBFIELDS: AN UPDATE

Alzheimer's & Dementia 2019年第7期15卷 P1549-P1550页

作者： Laura Wisse David Berron Rosanna Olsen Ana M. Daugherty Katrin Amunts Jean Augustinack Arnold Bakker Andrew Bender Marina Boccardi Martina Bocchetta Mallar Chakravarty Gaelle Chetelat Robin De Flores Jordan DeKraker Song-Lin Ding Ricardo Insausti Olga Kedo Susanne G. Mueller Noa Ofen Daniela Palombo Renaud La Joie Penn Image Computing and Science Laboratory (PICSL) University of Pennsylvania Philadelphia PA USA University of Pennsylvania Philadelphia PA USA Clinical Memory Research Unit Lund University Lund Sweden University of Toronto Toronto ON Canada Beckman Institute for Advanced Science and Technology Champaign IL USA Institute of Neuroscience and Medicine (INM-1) Jülich Germany Massachusetts General Hospital Charlestown MA USA Johns Hopkins School of Medicine Baltimore MD USA Michigan State University East Lansing MI USA IRCCS S Giovanni di Dio Fatebenefratelli Brescia Italy Dementia Research Centre Queen Square Institute of Neurology University College London London United Kingdom McGill University Montreal QC Canada Inserm UMR-S U1237 Université de Caen-Normandie Caen France The University of Western Ontario London ON Canada Allen Brain Institute Seattle WA USA University of Castilla-La Mancha Albacete Spain Forschungszentrum Jülich Julich Germany Center for Imaging of Neurodegenerative Diseases San Francisco CA USA Wayne State University Detroit MI USA Boston University School of Medicine Boston MA USA University of California San Francisco San Francisco CA USA

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P4-591: THE DEVELOPMENT OF A HARMONIZED SEGMENTATION PROTOCOL FOR HIPPOCAMPAL SUBFIELDS: AN UPDATE

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Alzheimer's & Dementia 2019年第7S_PART_30期15卷

作者： Laura Wisse David Berron Rosanna Olsen Ana M. Daugherty Katrin Amunts Jean Augustinack Arnold Bakker Andrew Bender Marina Boccardi Martina Bocchetta Mallar Chakravarty Gaelle Chetelat Robin De Flores Jordan DeKraker Song-Lin Ding Ricardo Insausti Olga Kedo Susanne G. Mueller Noa Ofen Daniela Palombo Naftali Raz Craig E. Stark Lei Wang Paul A. Yushkevich Qijing Yu Valerie A. Carr Renaud La Joie Penn Image Computing and Science Laboratory (PICSL) University of Pennsylvania Philadelphia PA USA University of Pennsylvania Philadelphia PA USA Clinical Memory Research Unit Lund University Lund Sweden University of Toronto Toronto ON Canada Beckman Institute for Advanced Science and Technology Champaign IL USA Institute of Neuroscience and Medicine (INM-1) Jülich Germany Massachusetts General Hospital Charlestown MA USA Johns Hopkins School of Medicine Baltimore MD USA Michigan State University East Lansing MI USA IRCCS S Giovanni di Dio Fatebenefratelli Brescia Italy Dementia Research Centre Queen Square Institute of Neurology University College London London United Kingdom McGill University Montreal QC Canada Inserm UMR-S U1237 Université de Caen-Normandie Caen France The University of Western Ontario London ON Canada Allen Brain Institute Seattle WA USA University of Castilla-La Mancha Albacete Spain Forschungszentrum Jülich Julich Germany Center for Imaging of Neurodegenerative Diseases San Francisco CA USA Wayne State University Detroit MI USA Boston University School of Medicine Boston MA USA University of California Irvine Irvine CA USA Northwestern University Chicago IL USA San Jose State University San Jose CA USA University of California San Francisco San Francisco CA USA

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The development of a valid, reliable, harmonized segmentation protocol for hippocampal subfields and medial temporal lobe cortices: A progress update

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Alzheimer's & Dementia 2020年第S4期16卷

作者： Renaud La Joie Rosanna Olsen David Berron Katrin Amunts Jean Augustinack Arnold Bakker Andrew Bender Marina Boccardi Martina Bocchetta M. Mallar Chakravarty Gael Chetelat Robin de Flores Jordan DeKraker Song-Lin Ding Ricardo Insausti Olga Kedo Susanne G Mueller Noa Ofen Daniela Palombo Naftali Raz Craig E. Stark Lei Wang Paul A. Yushkevich Qijing Yu Valerie A Carr Laura Wisse Ana M. Daugherty Memory and Aging Center UCSF Weill Institute for Neurosciences University of California San Francisco San Francisco CA USA University of Toronto Toronto ON Canada Clinical Memory Research Unit Lund University Lund Sweden Institute of Neuroscience and Medicine (INM-1) Jülich Germany Massachusetts General Hospital Charlestown MA USA Johns Hopkins School of Medicine Baltimore MD USA Michigan State University East Lansing MI USA IRCCS S. Giovanni di Dio Fatebenefratelli Brescia Italy Dementia Research Centre Queen Square Institute of Neurology University College London London United Kingdom Cerebral Imaging Centre - Douglas Mental Health University Institute Verdun QC Canada Inserm-EPHE-UCN U1077 Caen France Inserm UMR-S U1237 Université de Caen-Normandie GIP Cyceron Caen France The University of Western Ontario London ON Canada Allen Brain Institute Seattle WA USA University of Castilla-La Mancha Albacete Spain Forschungszentrum Jülich Julich Germany Center for Imaging of Neurodegenerative Diseases San Francisco CA USA Wayne State University Detroit MI USA Boston University School of Medicine Boston MA USA University of California Irvine Irvine CA USA Northwestern University Chicago IL USA Penn Image Computing and Science Laboratory (PICSL) University of Pennsylvania Philadelphia PA USA San Jose State University San Jose CA USA Beckman Institute for Advanced Science and Technology Champaign IL USA

Background The medial temporal lobe (MTL, i.e. hippocampus and adjacent cortices) is particularly vulnerable to age-related diseases: Alzheimer’s disease, other age-related proteinothies (TDP-43, AGD, etc) and vascular injury. Yet, the subregional pattern of vulnerability is thought to differ across etiologies; characterizing these differences using high-resolution MRI may provide more insight in disease processes and better biomarkers. However, substantial differences in subfield definition has hindered the ability to compare results across laboratories or draw robust conclusions (Figure 1). The Hippocampal Subfields Group (HSG) is an international group seeking to remedy this problem by developing a histologically-valid, reliable, and freely available segmentation protocol for high-resolution T2-weighted 3T MRI (http://***) Method Our workflow consists of five steps: 1) collecting histology samples labeled by multiple expert neuroanatomists to form a novel reference dataset to guide the development of the MRI segmentation protocol, 2) developing boundary definitions for each segment of the hippocampus, (head, body, and tail) and MTL cortices), 3) assessing HSG community agreement with boundary rules via online questionnaires and revising boundary rules based on questionnaire responses, and 4) testing reliability of the protocol definitions on multiple MRI datasets. Result For both the hippocampal body and head, we have developed a preliminary subfield segmentation protocol (i.e. completed steps 1-2, see Figure 2 for a histology slice segmented by three anatomists). Step 3 was piloted for the outer boundaries of the body (i.e., the anterior/posterior, medial/lateral, and superior/inferior boundaries) using an online questionnaire describing each of the proposed rules. 29 labs participated and consensus agreement was reached for all rules, with only minor changes being made to improve comprehension and clarity. We are now creating and admini

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Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge

arXiv

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arXiv 2024年

作者： LaBella, Dominic Baid, Ujjwal Khanna, Omaditya McBurney-Lin, Shan McLean, Ryan Nedelec, Pierre Rashid, Arif Tahon, Nourel Hoda Altes, Talissa Bhalerao, Radhika Dhemesh, Yaseen Godfrey, Devon Hilal, Fathi Floyd, Scott Janas, Anastasia Kazerooni, Anahita Fathi Kirkpatrick, John Kent, Collin Kofler, Florian Leu, Kevin Maleki, Nazanin Menze, Bjoern Pajot, Maxence Reitman, Zachary J. Rudie, Jeffrey D. Saluja, Rachit Velichko, Yury Wang, Chunhao Warman, Pranav Adewole, Maruf Albrecht, Jake Anazodo, Udunna Anwar, Syed Muhammad Bergquist, Timothy Chen, Sully Francis Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Khalili, Nastaran Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Liu, Xinyang Mahtabfar, Aria Meier, Zeke Moawad, Ahmed W. Mongan, John Piraud, Marie Shinohara, Russell Takeshi Wiggins, Walter F. Abayazeed, Aly H. Akinola, Rachel Jakab, András Bilello, Michel de Verdier, Maria Correia Crivellaro, Priscila Davatzikos, Christos Farahani, Keyvan Freymann, John Hess, Christopher Huang, Raymond Lohmann, Philipp Moassefi, Mana Pease, Matthew W. Vollmuth, Phillipp Sollmann, Nico Diffley, David Nandolia, Khanak K. Warren, Daniel I. Hussain, Ali Fehringer, Pascal Bronstein, Yulia Deptula, Lisa Stein, Evan G. Taherzadeh, Mahsa de Oliveira, Eduardo Portela Haughey, Aoife Kontzialis, Marinos Saba, Luca Turner, Benjamin Brüßeler, Melanie M.T. Ansari, Shehbaz Gkampenis, Athanasios Weiss, David Maximilian Mansour, Aya Shawali, Islam H. Yordanov, Nikolay Stein, Joel M. Hourani, Roula Moshebah, Mohammed Yahya Abouelatta, Ahmed Magdy Rizvi, Tanvir Willms, Klara Martin, Dann C. Okar, Abdullah D'Anna, Gennaro Taha, Ahmed Sharifi, Yasaman Faghani, Shahriar Kite, Dominic Pinho, Marco Haider, Muhammad Ammar Aristizabal, Alejandro Karargyris, Alexandros Kassem, Hasan Pati, Sarthak Sheller, Micah Alonso-Basanta, Michelle Villanueva-Meyer, Javier Rauschecker, Andreas M. Nada, Ayman Aboian, Mariam Flanders, Adam E. Wiestler, Benedikt Bakas, Spyridon Ca Duke University Medical Center Department of Radiation Oncology DurhamNC United States Division of Computational Pathology Department of Pathology Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Center for Federated Learning in Medicine Indiana University IndianapolisIN United States Department of Neurosurgery Thomas Jefferson University PhiladelphiaPA United States University of California San FranciscoCA United States Yale University New HavenCT United States Department of Radiation Oncology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University of Missouri ColumbiaMO United States Department of Biostatistics and Health Data Science Indiana University School of Medicine IndianapolisIN United States Children's Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Helmholtz AI Helmholtz Munich Germany Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Germany San FranciscoCA United States Biomedical Image Analysis and Machine Learning Department of Quantitative Biomedicine University of Zurich Switzerland Department of Neuroradiology Technical University of Munich Munich Germany University of San Diego CA United States Cornell University IthacaNY United States Department of Radiology Northwestern University EvanstonIL United States Duke University Medical Center School of Medicine DurhamNC United States Lab Crestview Radiology Lagos Nigeria Sage Bionetworks United States McGill University MontrealQC Canada Children's National Hospital WashingtonDC United States George Washington University WashingtonDC United State

We describe the design and results from the BraTS 2023 Intracranial Meningioma Segmentation Challenge. The BraTS Meningioma Challenge differed from prior BraTS Glioma challenges in that it focused on meningiomas, which are typically benign extra-axial tumors with diverse radiologic and anatomical presentation and a propensity for multiplicity. Nine participating teams each developed deep-learning automated segmentation models using image data from the largest multi-institutional systematically expert annotated multilabel multi-sequence meningioma MRI dataset to date, which included 1000 training set cases, 141 validation set cases, and 283 hidden test set cases. Each case included T2, T2/FLAIR, T1, and T1Gd brain MRI sequences with associated tumor compartment labels delineating enhancing tumor, non-enhancing tumor, and surrounding non-enhancing T2/FLAIR hyperintensity. Participant automated segmentation models were evaluated and ranked based on a scoring system evaluating lesion-wise metrics including dice similarity coefficient (DSC) and 95% Hausdorff Distance. The top ranked team had a lesion-wise median dice similarity coefficient (DSC) of 0.976, 0.976, and 0.964 for enhancing tumor, tumor core, and whole tumor, respectively and a corresponding average DSC of 0.899, 0.904, and 0.871, respectively. These results serve as state-of-the-art benchmarks for future pre-operative meningioma automated segmentation algorithms. Additionally, we found that 1286 of 1424 cases (90.3%) had at least 1 compartment voxel abutting the edge of the skull-stripped image edge, which requires further investigation into optimal pre-processing face anonymization steps. © 2024, CC BY.

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Publisher Correction: Neuroanatomical dimensions in medication-free individuals with major depressive disorder and treatment response to SSRI antidepressant medications or placebo

Nature Mental Health

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Nature Mental Health 2024年 1120页

作者： Cynthia H. Y. Fu Danilo Arnone Roland Zahn Allan H. Young Mathilde Antoniades Guray Erus Jose A. Garcia Yong Fan Haochang Shou Ashish Singh Christos Davatzikos Stephen R. Arnott Stephen C. Strother Taolin Chen Kun Qin Qiyong Gong Ki Sueng Choi Helen S. Mayberg Cherise Chin Fatt Madhukar H. Trivedi Benicio N. Frey Vibe G. Frokjaer Melanie Ganz Gitte M. Knudsen Beata R. Godlewska Catherine J. Harmer Stefanie Hassel Keith Ho Susan Rotzinger Sidney H. Kennedy Andrew M. McIntosh Aleks Stolicyn Heather C. Whalley Matthew D. Sacchet Jonathan Savitz Teresa A. Victor Martin P. Paulus Irina Strigo Duygu Tosun Dongtao Wei Jiang Qiu Toby Wise Ian M. Anderson J. F. William Deakin Rebecca Elliott W. Edward Craighead Boadie W. Dunlop Ian H. Gotlib Chao-Gan Yan School of Psychology University of East London London UK Centre for Affective Disorders Department of Psychological Medicine Institute of Psychiatry Psychology and Neuroscience King’s College London London UK South London and Maudsley NHS Foundation Trust Bethlem Royal Hospital London UK Center for Biomedical Image Computing and Analytics Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Penn Statistics in Imaging and Visualization Endeavor (PennSIVE) Center Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Philadelphia PA USA Rotman Research Institute Baycrest Centre Toronto Ontario Canada Department of Medical Biophysics University of Toronto Toronto Ontario Canada Huaxi MR Research Center Department of Radiology West China Hospital Sichuan University Chengdu China Research Unit of Psychoradiology Chinese Academy of Medical Sciences Chengdu China Department of Radiology Taihe Hospital Hubei University of Medicine Shiyan China Nash Family Center for Advanced Circuit Therapeutics Icahn School of Medicine at Mount Sinai New York NY USA Department of Psychiatry Center for Depression Research and Clinical Care University of Texas Southwestern Medical Center Dallas TX USA Department of Psychiatry and Behavioural Neurosciences McMaster University Hamilton Ontario Canada Mood Disorders Treatment and Research Centre and Women’s Health Concerns Clinic St Joseph’s Healthcare Hamilton Hamilton Ontario Canada Neurobiology Research Unit University Hospital Rigshospitalet Copenhagen Denmark Department of Clinical Medicine Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Department of Psychiatry Psychiatric Centre Copenhagen Copenhagen Denmark Department of Computer Science University of Copenhagen Copenhagen Denmark Department of Psychiatry University of Oxford Oxford UK Oxford Health NHS Foundation Trust Warneford Hospital Oxford UK Mathison Centre for Me

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