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Hippocampal subfields at ultra high field MRI: An overview of segmentation and measurement methods

Alessia Giuliano, Graziella Donatelli, Mirco Cosottini, Michela Tosetti, Alessandra Retico, Maria Evelina Fantacci
2017 Hippocampus  
The present review provides an overview of the manual, semi-automated and fully automated methods that allow the assessment of hippocampal subfield morphometry at UHF MRI, focusing on the different hippocampal  ...  Studying the morphometry of the hippocampus is crucial in neuroimaging research because changes in volume and thickness of hippocampal subregions may be relevant in the early assessment of pathological  ...  In this study, in addition to the measurement of the whole hippocampal body volume normalized to TIV, the authors developed a method to manually measure the thicknesses of the SRLM (CA1:SRLM) and of the  ... 
doi:10.1002/hipo.22717 pmid:28188659 pmcid:PMC5573987 fatcat:njiutzqnrfe7ldchxeehe2fs5y

Measurement of brain volume using MRI: software, techniques, choices and prerequisites

Simon S Keller, Neil Roberts
2009 Journal of Anthropological Sciences  
There dre numerous approaches for obtaining a brain volume estimate from MRI, and the primary focus of this paper is to provide an overview of the methods available to estimate the volume of three brain  ...  We provide information on choice of computer software, hardware compatibility, required user expertise, the application of manual and automated MR image analysis techniques, and anatomical guidelines,  ...  Automated techniques Unlike manual quantitative region of interest methods, semi-automated and automated methods do not require manual delineation of brain structures through a determined number MR sections  ... 
pmid:19663172 fatcat:fpm3xlohlbb47es5sgl7tk23fa

A comparison of automated segmentation and manual tracing for quantifying hippocampal and amygdala volumes

Rajendra A. Morey, Christopher M. Petty, Yuan Xu, Jasmeet Pannu Hayes, H. Ryan Wagner, Darrell V. Lewis, Kevin S. LaBar, Martin Styner, Gregory McCarthy
2009 NeuroImage  
Thus, our goal was to compare the performance of two popular and fully automated tools, FSL/FIRST and FreeSurfer, to expert hand tracing in the measurement of the hippocampus and amygdala.  ...  Compared to hand tracing, hippocampal measurements with FreeSurfer exhibited greater volume overlap, smaller volume difference, and higher correlation than FIRST, and sample size estimates with FreeSurfer  ...  ., and Srishti Seth, B.S.  ... 
doi:10.1016/j.neuroimage.2008.12.033 pmid:19162198 pmcid:PMC2714773 fatcat:jf2jmqmxgjbajfyxp5wok7jqdq


Susanne G. Mueller, Paul A. Yushkevich, Lei Wang, Koen van Leemput, Kate Alpert, Katrina Paz, Sandhitsu Das, Eugenio Iglesias, Michael W. Weiner
2016 Alzheimer's & Dementia  
The overall goal was to systematically compare the performance of five representative manual and automated T1 and T2 based subfield labeling techniques in a subset of the ADNI2 population.  ...  Objective: Subfield-specific measurements provide superior information in the early stages of neurodegenerative diseases compared to global hippocampal measurements.  ...  Acknowledgment The project was supported by a grant of the Alzheimer's Association (ADNI 2-12-233036) to MWW and SGM. None of the authors has a conflict of interest to declare.  ... 
doi:10.1016/j.jalz.2016.06.1399 fatcat:byhrkp5quzgpvc6gk3mxntnvee

Systematic comparison of different techniques to measure hippocampal subfield volumes in ADNI2

Susanne G. Mueller, Paul A. Yushkevich, Sandhitsu Das, Lei Wang, Koen Van Leemput, Juan Eugenio Iglesias, Kate Alpert, Adam Mezher, Peter Ng, Katrina Paz, Michael W. Weiner
2018 NeuroImage: Clinical  
The overall goal was to systematically compare the performance of five representative manual and automated T1 and T2 based subfield labeling techniques in a subset of the ADNI2 population.  ...  Objective: Subfield-specific measurements provide superior information in the early stages of neurodegenerative diseases compared to global hippocampal measurements.  ...  Acknowledgment The project was supported by a grant of the Alzheimer's Association (ADNI 2-12-233036) to MWW and SGM. None of the authors has a conflict of interest to declare.  ... 
doi:10.1016/j.nicl.2017.12.036 pmid:29527502 pmcid:PMC5842756 fatcat:sgtkjzsplrfdpebyvy744zgsce

A comparison of automated segmentation and manual tracing in estimating hippocampal volume in ischemic stroke and healthy control participants

Mohamed Salah Khlif, Natalia Egorova, Emilio Werden, Alberto Redolfi, Marina Boccardi, Charles S. DeCarli, Evan Fletcher, Baljeet Singh, Qi Li, Laura Bird, Amy Brodtmann
2019 NeuroImage: Clinical  
Manual quantification of the hippocampal atrophy state and rate is time consuming and prone to poor reproducibility, even when performed by neuroanatomical experts.  ...  Our first goal was to compare manual and automated hippocampal segmentation in ischemic stroke and to, secondly, study the impact of stroke lesion presence on hippocampal volume estimation.  ...  The authors acknowledge the facilities, and the scientific and technical assistance of the National Imaging Facility at the Florey Node. The authors would like to thank Mr. Oliver Martinez and Mr.  ... 
doi:10.1016/j.nicl.2018.10.019 pmid:30606656 pmcid:PMC6411582 fatcat:mc2lmg2x2fehblmrdxdvgfrhym

A Quantitative Imaging Biomarker Supporting Radiological Assessment of Hippocampal Sclerosis Derived From Deep Learning-Based Segmentation of T1w-MRI

Michael Rebsamen, Piotr Radojewski, Richard McKinley, Mauricio Reyes, Roland Wiest, Christian Rummel
2022 Frontiers in Neurology  
We investigate the sensitivity of automated segmentation methods to support radiological assessments of hippocampal sclerosis (HS).  ...  We calculated effect sizes (Cohen's d) between left/right HS and healthy controls based on the asymmetry of hippocampal volumes.  ...  Subsequently derived measures of the hippocampal shape and volume were calculated identically from the binary segmentation of the respective method.  ... 
doi:10.3389/fneur.2022.812432 pmid:35250818 pmcid:PMC8894898 fatcat:pefls3t7kngfvesejxxrxzjpri

Automatic multispectral MRI segmentation of human hippocampal subfields: an evaluation of multicentric test–retest reproducibility

Andrea Chiappiniello, Roberto Tarducci, Cristina Muscio, Maria Grazia Bruzzone, Marco Bozzali, Pietro Tiraboschi, Anna Nigri, Claudia Ambrosi, Elena Chipi, Stefania Ferraro, Cristina Festari, Roberto Gasparotti (+11 others)
2020 Brain Structure and Function  
AbstractAccurate and reproducible automated segmentation of human hippocampal subfields is of interest to study their roles in cognitive functions and disease processes.  ...  Multispectral structural MRI methods have been proposed to improve automated hippocampal subfield segmentation accuracy, but the reproducibility in a multicentric setting is, to date, not well characterized  ...  Acknowledgements This work was supported by the Italian Minister  ... 
doi:10.1007/s00429-020-02172-w pmid:33231744 fatcat:lgbumqbh5zdhzoojj76qqoicn4

A comprehensive testing protocol for MRI neuroanatomical segmentation techniques: Evaluation of a novel lateral ventricle segmentation method

Matthew J. Kempton, Tracy S.A. Underwood, Simon Brunton, Floris Stylios, Anne Schmechtig, Ulrich Ettinger, Marcus S. Smith, Simon Lovestone, William R. Crum, Sophia Frangou, Steven C.R. Williams, Andrew Simmons
2011 NeuroImage  
The testing protocol produced quantitative measures of accuracy, reliability and sensitivity of lateral ventricle volume estimates for each segmentation method.  ...  Accuracy is assessed in infants, young adults and patients with Alzheimer's disease in comparison to gold standard measures by expert observers using a manual technique based on Cavalieri's principle.  ...  NHS Foundation Trust and the Institute of Psychiatry, King's College London.  ... 
doi:10.1016/j.neuroimage.2011.06.080 pmid:21835253 pmcid:PMC3551263 fatcat:htqvnhsl4ba4nadvaneompt4ke

A Methodology for Systematic Volumetric Analysis of Perioperative Cranial Imaging in Neurosurgical Patients

Kofi-Buaku Atsina, Richard Gorniak, Ashwini Sharan, Chengyuan Wu
2016 JHN Journal  
Although objective assessment of perioperative imaging provides a rigorous evaluation method of neurosurgical techniques in epilepsy, its use remains far from mainstream.  ...  The percentage of each structure affected was calculated, using a voxel by voxel comparison. Results We were successfully able to determine ablation volumes and critically evaluate laser placement.  ...  ACKNOWLEDGEMENTS No financial support was required in the preparation of this manuscript.  ... 
doi:10.29046/jhnj.011.2.002 fatcat:gbzk4752fbditn2dkugvzl7zie

Neuroanatomical Risk Factors for Post Traumatic Stress Disorder (PTSD) in Recent Trauma Survivors [article]

Ziv Ben-Zion, Moran Artzi, Dana Niry, Jackob Nimrod Keynan, Roee Admon, Haggai Sharon, Pinchas Halpern, Israel Liberzon, Arieh Shalev, Talma Hendler
2019 bioRxiv   pre-print
Hippocampus and CSP volumes were extracted automatically by FreeSurfer and verified manually, and correlated with PTSD severity at each time point.  ...  We hypothesized that at one-month post-trauma, the relation between hippocampal volume and PTSD severity would be moderated by CSP volume, and that this early interaction would account for persistent PTSD  ...  Acknowledgments: This work was supported by award number R01MH-103287 from the National  ... 
doi:10.1101/721134 fatcat:6muli5mktrekhmueq6kiunrjfy

On brain atlas choice and automatic segmentation methods: a comparison of MAPER & FreeSurfer using three atlas databases

Siti Nurbaya Yaakub, Rolf A. Heckemann, Simon S. Keller, Colm J. McGinnity, Bernd Weber, Alexander Hammers
2020 Scientific Reports  
For each combination of atlas and method, we conducted a leave-one-out cross-comparison to estimate the segmentation accuracy of FreeSurfer and MAPER.  ...  MAPER was better than FreeSurfer at modelling manual segmentations in the healthy control leave-one-out analyses in two of the three atlas databases, and the Hammers_mith atlas database transferred to  ...  As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report.  ... 
doi:10.1038/s41598-020-57951-6 pmid:32071355 pmcid:PMC7028906 fatcat:sntxfhkpsrh3xlmb7pxxoa6tju

Technical and clinical validation of commercial automated volumetric MRI tools for dementia diagnosis—a systematic review

Hugh G. Pemberton, Lara A. M. Zaki, Olivia Goodkin, Ravi K. Das, Rebecca M. E. Steketee, Frederik Barkhof, Meike W. Vernooij
2021 Neuroradiology  
The quantitative neuroradiology initiative (QNI) framework highlights six necessary steps for the development, validation and integration of quantitative tools in the clinic.  ...  Our intention is to assist neuroradiologists in making informed decisions regarding the adoption of these methods in the clinic.  ...  Acknowledgements The authors would like to thank all vendors for their participation and provision of product details.  ... 
doi:10.1007/s00234-021-02746-3 pmid:34476511 pmcid:PMC8528755 fatcat:fe3qj4k2qfal3ozx23ondg3r4e

A direct morphometric comparison of five labeling protocols for multi-atlas driven automatic segmentation of the hippocampus in Alzheimer's disease

Sean M. Nestor, Erin Gibson, Fu-Qiang Gao, Alex Kiss, Sandra E. Black
2013 NeuroImage  
Hippocampal volumetry derived from structural MRI is increasingly used to delineate regions of interest for functional measurements, assess efficacy in therapeutic trials of Alzheimer's disease (AD) and  ...  Recent developments in automated volumetry commonly use multi-template fusion driven by expert manual labels, enabling highly accurate and reproducible segmentation in disease and healthy subjects.  ...  The development and testing of the hippocampal segmentation algorithm was supported by several grants, most notably from the Canadian Institutes of Health Research (MT#13129), the Alzheimer Society of  ... 
doi:10.1016/j.neuroimage.2012.10.081 pmid:23142652 pmcid:PMC3606906 fatcat:l4je6rxxjjdvdj2gqjampsjnii

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain-behavior relationships after stroke

Sook-Lei Liew, Artemis Zavaliangos-Petropulu, Neda Jahanshad, Catherine E Lang, Kathryn S Hayward, Keith R Lohse, Julia M Juliano, Francesca Assogna, Lee A Baugh, Anup K Bhattacharya, Bavrina Bigjahan, Michael R Borich (+55 others)
2020 Human Brain Mapping  
This article outlines the efforts taken by the ENIGMA Stroke Recovery working group to develop neuroinformatics protocols and methods to manage multisite stroke brain magnetic resonance imaging, behavioral  ...  The goal of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well-powered meta- and mega-analytic  ...  with an emphasis on reliable and reproducible methods.  ... 
doi:10.1002/hbm.25015 pmid:32310331 pmcid:PMC8675421 fatcat:lvelmlkkzrf2nemyl6jqbdqsqq
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