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Automated Olfactory Bulb Segmentation on High Resolutional T2-Weighted MRI

Santiago Estrada, Ran Lu, Kersten Diers, Weiyi Zeng, Philipp Ehses, Tony Stöcker, Monique M.B Breteler, Martin Reuter
2021 NeuroImage  
The neuroimage analysis community has neglected the automated segmentation of the olfactory bulb (OB) despite its crucial role in olfactory function.  ...  In this work, we introduce a novel, fast, and fully automated deep learning pipeline to accurately segment OB tissue on sub-millimeter T2-weighted (T2w) whole-brain MR images.  ...  to segment and quantify the olfactory bulb on high resolutional T2-weighted MR scans.  ... 
doi:10.1016/j.neuroimage.2021.118464 pmid:34389442 pmcid:PMC8473894 fatcat:mjdflu6bqzfdpawwklyntlsggy

Automated Olfactory Bulb Segmentation on High Resolutional T2-Weighted MRI [article]

Santiago Estrada, Ran Lu, Kersten Diers, Weiyi Zeng, Philipp Ehses, Tony Stöcker, Monique M.B Breteler, Martin Reuter
2021 arXiv   pre-print
In this work, we introduce a novel, fast, and fully automated deep learning pipeline to accurately segment OB tissue on sub-millimeter T2-weighted (T2w) whole-brain MR images.  ...  The neuroimage analysis community has neglected the automated segmentation of the olfactory bulb (OB) despite its crucial role in olfactory function.  ...  Olfactory Bulb Pipeline Our proposed deep learning method is aimed at segmenting the OB on high-resolutional T2w whole-brain MRI.  ... 
arXiv:2108.04267v1 fatcat:wiqs3hlpyrhjjic7owjp3rdyhu

Automatic Segmentation of the Olfactory Bulb

Dmitriy Desser, Francisca Assunção, Xiaoguang Yan, Victor Alves, Henrique Fernandes, Thomas Hummel
2021 Brain Sciences  
In conclusion, we present a newly developed ready-to-use tool that can perform the segmentation of OBs based on multimodal data consisting of T1 whole-brain images and T2 coronal high-resolution images  ...  In order to develop a stable and versatile algorithm and to train the neural network, we used four datasets consisting of whole-brain T1 and high-resolution T2 MRI scans, as well as the corresponding clinical  ...  The following two modalities were used in this study: T1-weighted axial whole-brain scans and T2-weighted high-resolution coronal scans for OB imaging.  ... 
doi:10.3390/brainsci11091141 pmid:34573163 pmcid:PMC8471091 fatcat:rbsk4nagffedbicyja2xyy6oum

The association between olfactory bulb volume, cognitive dysfunction, physical disability and depression in multiple sclerosis

Ö. Yaldizli, I.-K. Penner, T. Yonekawa, Y. Naegelin, J. Kuhle, M. Pardini, D. T. Chard, C. Stippich, J.-i. Kira, K. Bendfeldt, M. Amann, E.-W. Radue (+2 others)
2015 European Journal of Neurology  
The olfactory bulb was semi-automatically segmented on high-resolution 3D T1-weighted MRI.  ...  MRI analysis MS lesions (T2-weighted hyperintense and T1-weighted hypointense lesions), and the olfactory bulb on the MPRAGE scan, were segmented using the semiautomated thresholding tool in AMIRA (Version  ... 
doi:10.1111/ene.12891 pmid:26699999 fatcat:ckeflubptfh43en73o5laqr3lu

Reduced Olfactory Bulb Volume Accompanies Smelling Dysfunction After Mild SARS-CoV-2 Infection: The Hamburg City Health Study COVID Program [article]

Marvin Petersen, Benjamin T. Becker, Maximilian Schell, Carola Mayer, Felix L. Naegele, Elina Petersen, Raphael Twerenbold, Goetz Thomalla, Bastian Cheng, Christian Betz, Anna Sophie Hoffmann
2022 medRxiv   pre-print
Automated olfactory bulb volumetry was performed on T2-weighted MR imaging data. Olfactory function was assessed longitudinally after recruitment and at follow-up via a structured questionnaire.  ...  Despite its high prevalence, the determinants of smelling impairment in COVID-19 remain opaque.  ...  Olfactory bulb segmentation We performed OB segmentation on high-resolution T2-weighted images leveraging a novel fully-automated deep learning-based pipeline specifically designed for OB volumetry (28  ... 
doi:10.1101/2022.07.24.22277973 fatcat:dpg37x5d5zhefatlptioqamiq4

Mapping the Microstructure and Striae of the Human Olfactory Tract with Diffusion MRI

Shiloh L. Echevarria-Cooper, Guangyu Zhou, Christina Zelano, Franco Pestilli, Todd B. Parrish, Thorsten Kahnt
2021 Journal of Neuroscience  
Here, we used a dMRI method with readout segmentation of long variable echo-trains (RESOLVE) to minimize image distortions and characterize the human olfactory tracts in vivo We collected high-resolution  ...  The olfactory tracts project from the olfactory bulb along the base of the frontal cortex, branching into several striae to meet diverse cortical regions.  ...  The ROIs were drawn for the left and right hemispheres separately on each individual's anatomical images. The olfactory bulbs were outlined on each individual's 0.5 mm resolution T2-weighted image.  ... 
doi:10.1523/jneurosci.1552-21.2021 pmid:34759031 pmcid:PMC8741165 fatcat:vqkakwt5lnea3a454ozevqzivm

3D mapping of neuronal migration in the embryonic mouse brain with magnetic resonance microimaging

Abby E. Deans, Youssef Zaim Wadghiri, Orlando Aristizábal, Daniel H. Turnbull
2015 NeuroImage  
A striking example is provided by NP cells born in the ventral forebrain of mid-gestation stage mice, which subsequently migrate long distances to their final positions in the cortex and olfactory bulb  ...  segmentation of the labeled cells.  ...  Marc Fuccillo and Gordon Fishell for advice on MGE/LGE cell migration and assistance with the immunohistochemistry.  ... 
doi:10.1016/j.neuroimage.2015.04.010 pmid:25869862 pmcid:PMC4446241 fatcat:6c34trlnzjbz3okoizpghdiecq

RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI

Ipek Oguz, Honghai Zhang, Ashley Rumple, Milan Sonka
2014 Journal of Neuroscience Methods  
Comparative results obtained on two challenging in vivo datasets, consisting of 22 T1-weighted rat brain images and 10 T2-weighted mouse brain images illustrate the robustness and excellent performance  ...  High-field MRI is a popular technique for the study of rodent brains. These datasets, while similar to human brain MRI in many aspects, present unique image processing challenges.  ...  RATS achieves satisfactory results even in the worst case, with minor defects near the olfactory bulb. 3D brain segmentation on the worst-case subject for the T1-weighted in vivo rat dataset: pink: PCNN  ... 
doi:10.1016/j.jneumeth.2013.09.021 pmid:24140478 pmcid:PMC3914765 fatcat:v6aec26ib5hotinectynsegn7e

3D U-Net improves automatic brain extraction for isotropic rat brain MRI data [article]

Li-Ming Hsu, Shuai Wang, Lindsay Walton, Tzu-Wen Winnie Wang, Sung-Ho Lee, Yen-Yu Ian Shih
2021 bioRxiv   pre-print
We trained and validated our model using a recently released CAMRI rat brain database acquired at isotropic spatial resolution, including T2-weighted turbo-spin-echo structural MRI and T2*-weighted echo-planar-imaging  ...  We trust that this tool will avoid human bias and streamline pre-processing steps during 3D high resolution rodent brain MRI data analysis.  ...  ., 2021) , including T2-weighted (T2w) rapid acquisition with relaxation enhancement (RARE) structural MRI (0.2 mm isotropic resolution) and T2*-weighted (T2*w) echo-planar-imaging (EPI) functional MRI  ... 
doi:10.1101/2021.09.27.462020 fatcat:jamak3jv2rf37am5ne64vzvp7i

Volumes of brain structures in captive wild-type and laboratory rats: 7T magnetic resonance in vivo automatic atlas-based study

Marlena Welniak–Kaminska, Michal Fiedorowicz, Jaroslaw Orzel, Piotr Bogorodzki, Klaudia Modlinska, Rafal Stryjek, Anna Chrzanowska, Wojciech Pisula, Pawel Grieb, Grainne Mary McAlonan
2019 PLoS ONE  
High resolution T2-weighted images of brains of adult male Warsaw Wild Captive Pisula-Stryjek rats (WWCPS, a model of wild type), laboratory pigmented (Brown Norway strain, BN) and albino rats (Wistar  ...  These alterations certainly occurred on the background of modifications in brain morphology.  ...  resolution T2-weighted images were intensity corrected and automatically segmented for white matter, grey matter and cerebrospinal fluid.  ... 
doi:10.1371/journal.pone.0215348 pmid:30973956 pmcid:PMC6459519 fatcat:ojsobimc2vf6dnco64icyk7wsm

atlasBREX: Automated template-derived brain extraction in animal MRI

Johannes Lohmeier, Takaaki Kaneko, Bernd Hamm, Marcus R. Makowski, Hideyuki Okano
2019 Scientific Reports  
MRI protocols (T1, T2).  ...  We proposed a generic template-derived approach for (semi-) automated brain extraction in animal MRI studies and evaluated our implementation with different animal models (macaque, marmoset, rodent) and  ...  In contrast, ABX presented accurate segmentation of the marmoset brain, illustrated with brain models in Fig. 5b ,d, respectively panel α, particularly with regard to the olfactory bulb. evaluation with  ... 
doi:10.1038/s41598-019-48489-3 pmid:31434923 pmcid:PMC6704255 fatcat:o5fsfpyegzbd5o5jpiirc465fe

Brain orchestration of pregnancy and maternal behavior in mice: a longitudinal morphometric study

David André Barrière, Arsène Ella, Frédéric Szeremeta, Hans Adriaensen, William Même, Elodie Chaillou, Martine Migaud, Sandra Même, Frédéric Lévy, Matthieu Keller
2021 NeuroImage  
Here, we describe a longitudinal morphometric neuroimaging study in female mice between pre-gestation and weaning, using new magnetic resonance imaging (MRI) resources comprising a high-resolution brain  ...  template, its associated tissue priors (60-µm isotropic resolution) and a corresponding mouse brain atlas (1320 regions of interest).  ...  T 2 -weighted images were acquired using a 3D fast large-angle spin-echo (FLASE) sequence which allows 3D brain mapping with a high resolution in a suitable time for in vivo acquisition ( DiIorio et al  ... 
doi:10.1016/j.neuroimage.2021.117776 pmid:33516895 fatcat:y7oyrhwfv5bp5a5wyhyt6pza2q

Adapting the UK Biobank Brain Imaging Protocol and Analysis Pipeline for the C-MORE Multi-Organ Study of COVID-19 Survivors

Ludovica Griffanti, Betty Raman, Fidel Alfaro-Almagro, Nicola Filippini, Mark Philip Cassar, Fintan Sheerin, Thomas W. Okell, Flora A. Kennedy McConnell, Michael A. Chappell, Chaoyue Wang, Christoph Arthofer, Frederik J. Lange (+8 others)
2021 Frontiers in Neurology  
The protocol acquires high resolution T1, T2-FLAIR, diffusion weighted images, susceptibility weighted images, and arterial spin labelling data in 17 min.  ...  The automated imaging pipeline derives 1,575 IDPs, assessing brain anatomy (including olfactory bulb volume and intensity) and tissue perfusion, hyperintensities, diffusivity, and susceptibility.  ...  The protocol acquires high resolution T 1 , T 2 -FLAIR, diffusion weighted images, susceptibility weighted images, and arterial spin labelling data in 17 min.  ... 
doi:10.3389/fneur.2021.753284 pmid:34777224 pmcid:PMC8586081 fatcat:4budtjochrbwjkkobyu7sndi4u

Semi-automated 3D segmentation of major tracts in the rat brain: comparing DTI with standard histological methods

Erika Gyengesi, Evan Calabrese, Matthew C. Sherrier, G. Allan Johnson, George Paxinos, Charles Watson
2013 Brain Structure and Function  
We analysed 12 major white matter pathways using semi-automated tractography-based segmentation alongside manual segmentation of Gallyas silver-stained histology sections.  ...  With the increasing popularity of small animal MRI techniques, including diffusion tensor imaging (DTI), there is considerable interest in rapid segmentation methods of neurological structures for quantitative  ...  In general, white matter appears dark on T2*weighted MRI due to its relatively short T2* relaxation time, which may in turn be a result of the diamagnetic properties of myelin (Renshaw et al. 1986; Koenig  ... 
doi:10.1007/s00429-013-0516-8 pmid:23455647 pmcid:PMC3815507 fatcat:gm3fz7cpq5bwbhtoegdg6lhabu

In vivo 3D digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy

Yu Ma
2008 Frontiers in Neuroanatomy  
Based on these fi ndings we conclude that although in vitro datasets, compared to in vivo images, offer higher spatial resolutions, superior SNR and CNR, leading to improved image segmentation, in vivo  ...  C57BL/6J adult mouse brains were imaged in vivo on a 9.4 Tesla MR instrument at an isotropic spatial resolution of 100 µm.  ...  In our previous in vitro mouse brain atlas MRM study, we were also able to identify 20 brain regions on the T2*-weighted high resolution images (47 µm isotropic) which were acquired on a 17.6T MR instrument  ... 
doi:10.3389/neuro.05.001.2008 pmid:18958199 pmcid:PMC2525925 fatcat:7kyzpumoizdf5bkebecjvuaze4
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