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MRI analysis for hippocampus segmentation on a distributed infrastructure

S. Tangaro, N. Amoroso, M. Antonacci, M. Boccardi, M. Bocchetta, A. Chincarini, D. Diacono, G. Donvito, R. Errico, G. B. Frisoni, T. Maggipinto, A. Monaco (+3 others)
2016 2016 IEEE International Symposium on Medical Measurements and Applications (MeMeA)  
In this paper we implemented a complete segmentation pipeline in brain magnetic resonance imaging (MRI).  ...  In this article we present a general approach to submit and monitor workflows on distributed infrastructures using LONI Pipeline, including European Grid Infrastructure (EGI) and Torquebased batch farm  ...  the hippocampus on structural MRI.  ... 
doi:10.1109/memea.2016.7533716 dblp:conf/memea/TangaroAABBCDDE16 fatcat:yvd6ddajyfawdej6nzmwjthepe

A transfer-learning approach for first-year developmental infant brain segmentation using deep neural networks [article]

Yun Wang, Fateme Sadat Haghpanah, Natalie Aw, Andrew Laine, Jonathan Posner
2020 bioRxiv   pre-print
In this paper, we propose a transfer-learning approach based on convolutional neural network (CNN)-based image segmentation architecture, QuickNAT, to segment brain structures for newborns and 6-month  ...  Moreover, we demonstrated improved hippocampus segmentation performance via our approach in preterm infants.  ...  For our beloved friends, Pouneh Gorji and Arash Pourzarabi, two of the kindest souls living on the earth.  ... 
doi:10.1101/2020.05.22.110619 fatcat:7pt5t5fvvrbydj4h3fxh53nzqe

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  
FreeSurfer, FSL, and a DL-based method were applied for brain anatomy segmentation.  ...  Results from FreeSurfer and FSL-FIRST are contrasted to a deep learning (DL)-based segmentation method.Materials and MethodsWe used T1-weighted MRI scans from 105 patients with epilepsy and 354 healthy  ...  , reported for FreeSurfer on a very large cohort (mean AI of -0.007, identical to the result of our method for a 40-fold smaller sample of controls) (28), using manual tracing (62) , and in a meta-analysis  ... 
doi:10.3389/fneur.2022.812432 pmid:35250818 pmcid:PMC8894898 fatcat:pefls3t7kngfvesejxxrxzjpri

Etiology of hippocampal sclerosis: Evidence for a predisposing familial morphologic anomaly

M.-H. Tsai, H. R. Pardoe, Y. Perchyonok, G. J. Fitt, I. E. Scheffer, G. D. Jackson, S. F. Berkovic
2013 Neurology  
None of the first-degree relatives had HS on visual analysis and T2 relaxation times were normal, excluding the presence of HS.  ...  Left and right hippocampal volumes and T2 relaxometry were measured using 3-tesla MRI.  ...  , Florey Institute of Neuroscience and Mental Health), for their technical assistance.  ... 
doi:10.1212/wnl.0b013e31829a33ac pmid:23749796 pmcid:PMC3770171 fatcat:yy3mshuoq5ewdcbhsus55zqmyi

MRI morphology of the hippocampus in drug-resistant temporal lobe epilepsy: Shape inflation of left hippocampus and correlation of right-sided hippocampal volume and shape with visuospatial function in patients with right-sided TLE

Jae-Gon Yoo, David Jakabek, Hanna Ljung, Dennis Velakoulis, Danielle van Westen, Jeffrey C.L. Looi, Kristina Källén
2019 Journal of clinical neuroscience  
We manually segmented MRI of the hippocampus of participants using ANALYZE 11.0 software; and analysed hippocampal shape using SPHARM-PDM software.  ...  Decreased hippocampal volume was correlated with poorer performance on these tasks. The morphology of the hippocampus can be quantified via neuroimaging shape analysis in TLE.  ...  KK's research time was funded by: a Stig and Ragna Gorthons research grant; and a Region Skånes project grant.  ... 
doi:10.1016/j.jocn.2019.06.019 fatcat:5umrx76ob5hhzhwdr4hkx6h5wu

ANSH: Multimodal Neuroimaging Database Including MR Spectroscopic Data From Each Continent to Advance Alzheimer's Disease Research

Pravat K. Mandal, Kanika Sandal, Deepika Shukla, Manjari Tripathi, Kuldeep Singh, Saurav Roy
2020 Frontiers in Neuroinformatics  
ANSH is supported by a JAVA-based workflow environment and python providing a simple, dynamic, and distributed platform with data security.  ...  ., MRI, functional MRI, PET etc.) is extensively used to identify the causal molecular process for AD.  ...  Komal Jindal (Senior R&D Engineer, NINS lab) for critical comments and editorial support. PM and DS dedicate this article to their parents.  ... 
doi:10.3389/fninf.2020.571039 fatcat:3jk3oiw2pbafdazykbg5q5ka6u

Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) using Multi-Contrast MRI [article]

Thomas B Shaw, Steffen Bollmann, Ashley York, Maryam Ziaei, Markus Barth
2019 bioRxiv   pre-print
The volumetric and morphometric examination of hippocampus formation subfields in a longitudinal manner using in vivo MRI could lead to more sensitive biomarkers for neuropsychiatric disorders and diseases  ...  We examined the performance of a new longitudinal pipeline (Longitudinal Automatic Segmentation of Hippocampus Subfields [LASHiS]) against three freely available, published approaches.  ...  Acknowledgements The authors acknowledge the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy  ... 
doi:10.1101/759217 fatcat:34pid5v56rgmrjgbfmf5bfslmi

Diffusion tensor imaging reveals microstructural alterations in corpus callosum and associated transcallosal fiber tracts in adult macaques with neonatal hippocampal lesions

Yuguang Meng, Xiaoping Hu, Xiaodong Zhang, Jocelyne Bachevalier
2018 Hippocampus  
and splenium) for data analysis.  ...  The findings may provide complementary information for understanding the neural substrate of behavioral and cognitive deficits observed in patients with early insult to the hippocampus.  ...  We would like to thank Sudeep Patel for MRI data acquisition, Ruth Connelly and Doty Kempf (DVM) for assistance with animal care during neuroimaging procedures.  ... 
doi:10.1002/hipo.23006 pmid:29978933 pmcid:PMC6282702 fatcat:aq5fbjpajrevjflug7cac444wq

A game for crowdsourcing the segmentation of BigBrain data

Arno Klein
2016 Research Ideas and Outcomes  
Both these systems opperate on cloud-based infrastructure.  ...  For our first exploratory aim, will explore how our approach generalizes to all other brain regions, and for our second exploratory aim, we will train a supervised learning algorithm on the crowdsourced  ...  MRI segmentation (expected in 2016-2017).  ... 
doi:10.3897/rio.2.e8816 fatcat:jmilpqohufdtndugsmdqyp65py

The Rotterdam Scan Study: design update 2016 and main findings

M. Arfan Ikram, Aad van der Lugt, Wiro J. Niessen, Peter J. Koudstaal, Gabriel P. Krestin, Albert Hofman, Daniel Bos, Meike W. Vernooij
2015 European Journal of Epidemiology  
Imaging plays an essential role in research on neurological diseases in the elderly.  ...  Finally, we provide recommendations for future research, which will also be topics of investigation in the Rotterdam Scan Study.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://crea, which permits unrestricted use, distribution  ... 
doi:10.1007/s10654-015-0105-7 pmid:26650042 pmcid:PMC4690838 fatcat:ufywuzkeejdarhvdxcj4cgwpte

Imaging informatics for personalised medicine: applications and challenges

Tianming Liu, Hanchuan Peng, Xiaobo Zhou
2009 International Journal of Functional Informatics and Personalised Medicine  
His recent work has been focusing on building single-neuron whole-brain level 3D digital atlases for animals including C. elegans and fruitfly.  ...  He is also known for his minimum-redundant feature selection algorithm.  ...  For example, a recent comparison study (Babalola et al., 2008) reported that, for state-of-the-art methods, the Dice Coefficients (compared with manual segmentation) are around 70% for amygdale and hippocampus  ... 
doi:10.1504/ijfipm.2009.027587 pmid:19862353 pmcid:PMC2767191 fatcat:akhsnhq6kvdwjej4b6gezniwqy

Neuroimaging in Iran: A Review

G. Ali Hossein-Zadeh, Hamid Soltanian-Zadeh
2010 Basic and Clinical Neuroscience  
This is a challenge that cannot be solved without specific plans, policies, and funding.  ...  This paper presents an overview of the neuroimaging research in Iran in recent years, partitioned into three categories: anatomical imaging anatomical image analysis and functional imaging and analysis  ...  For group analysis of the fMRI data, S, Ghassemian, H. (2007). MRI and PET images fusion based on human retina model. Journal of Zhejiang Univ. Sci. A 8, 1624-1632.  ... 
doaj:f0ab5bedcd944608a1cb026e9ffb91ad fatcat:kqwkfhowyzad3ptjoizidl2p4m

Automatic segmentation of the hippocampus for preterm neonates from early-in-life to term-equivalent age

Ting Guo, Julie L. Winterburn, Jon Pipitone, Emma G. Duerden, Min Tae M. Park, Vann Chau, Kenneth J. Poskitt, Ruth E. Grunau, Anne Synnes, Steven P. Miller, M. Mallar Chakravarty
2015 NeuroImage: Clinical  
Methods: First, we present a three-step manual segmentation protocol to delineate the hippocampus for preterm neonates and apply this protocol on 22 early-in-life and 22 term images.  ...  To date, segmentation of the hippocampus for preterm-born neonates has not yet been performed early-in-life (shortly after birth when clinically stable).  ...  The days of life (DOL) at the time of the MRI scans was considered as a covariate in the analysis.  ... 
doi:10.1016/j.nicl.2015.07.019 pmid:26740912 pmcid:PMC4561668 fatcat:upmc2zatgnbodb3sn3gaz64nqu

Structural variation in hippocampal dentations among healthy young adults [article]

Julia ten Hove, Jordan Poppenk
2020 bioRxiv   pre-print
is based on a single small study.  ...  Little is known about the hippocampus dentations - or "bumps" on the inferior surface of the hippocampus - and whether they hold functional significance.  ...  Biorac for assistance  ... 
doi:10.1101/2020.02.09.940726 fatcat:kwwf7ns7yfgtna3jsy3eszauyu

Ontario Neurodegenerative Disease Research Initiative (ONDRI): Structural MRI Methods and Outcome Measures

Joel Ramirez, Melissa F. Holmes, Christopher J. M. Scott, Miracle Ozzoude, Sabrina Adamo, Gregory M. Szilagyi, Maged Goubran, Fuqiang Gao, Stephen R. Arnott, Jane M. Lawrence-Dewar, Derek Beaton, Stephen C. Strother (+7 others)
2020 Frontiers in Neurology  
The Ontario Neurodegenerative Research Initiative (ONDRI) is a 3 years multi-site prospective cohort study that has acquired comprehensive multiple assessment platform data, including 3T structural MRI  ...  To effectively quantify regional measures of normal and pathological brain tissue volumes, the ONDRI neuroimaging platform implemented a semi-automated MRI processing pipeline that was able to address  ...  ACKNOWLEDGMENTS We would like to thank the ONDRI participants for the time, consent, and participation in our study. Thank you to the L.C.  ... 
doi:10.3389/fneur.2020.00847 pmid:32849254 pmcid:PMC7431907 fatcat:pqfbaq5skzax3iezfqs5i42squ
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