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Automated segmentation of the substantia nigra, subthalamic nucleus and red nucleus in 7 T data at young and old age

Eelke Visser, Max C. Keuken, Birte U. Forstmann, Mark Jenkinson
2016 NeuroImage  
With recent developments in MR acquisition at 7 T, smaller brainstem structures such as the red nuclei, substantia nigra and subthalamic nuclei can be imaged with good contrast and resolution.  ...  We perform a vertex-based analysis to identify changes with age in the shape of the structures and present results suggesting that the method may be at least as effective as manual delineation in capturing  ...  Acknowledgements We wish to thank the Wellcome Trust for funding through the Strategic Award for "Integrated multimodal brain imaging for neuroscience research and clinical practice" (grant number 098369  ... 
doi:10.1016/j.neuroimage.2016.06.039 pmid:27349329 pmcid:PMC4988791 fatcat:swz5od4ru5h27c4ctsts5akxma

Age-related magnetic susceptibility changes in deep grey matter and cerebral cortex of normal young and middle-aged adults depicted by whole brain analysis

Romana Burgetova, Petr Dusek, Andrea Burgetova, Adam Pudlac, Manuela Vaneckova, Dana Horakova, Jan Krasensky, Zsoka Varga, Lukas Lambert
2021 Quantitative Imaging in Medicine and Surgery  
Deep grey matter structures with the highest increase of susceptibility values with age included the red nucleus, putamen, substantia nigra, dentate nucleus, external globus pallidus, caudate nucleus,  ...  and the subthalamic nucleus in decreasing order.  ...  , putamen, caudate nucleus, thalamus, pulvinar, substantia nigra, red nucleus, dentate nucleus, subthalamic nucleus, and total white matter ( Figure 1 ).  ... 
doi:10.21037/qims-21-87 pmid:34476177 pmcid:PMC8339659 fatcat:xvgh7xiszrbpte7jb3fhw4vmjm

Charting human subcortical maturation with in vivo 7 T MRI [article]

Steven Miletic, Pierre-Louis Bazin, Scott J.S. Isherwood, Max Keuken, Anneke Alkemade, Birte Forstmann
2021 bioRxiv   pre-print
Here, we zoom in on 17 prominent subcortical structures, by describing their approximate iron and myelin contents and thickness, and by providing detailed accounts of their age-related changes across the  ...  The results provide compelling insights into the highly heterogeneous mor- phometry and intricate age-related variations of these structures.  ...  Acknowledgements This research was financially supported by STW/NWO (#14017; BUF and AA), ERC PoC (BUF), NWO Vici (016.Vici.185.052; BUF). CRediT author statement  ... 
doi:10.1101/2021.04.07.438765 fatcat:e3vnstthqff25cj4txw4wkgtsa

Quantitative age-dependent differences in human brainstem myelination assessed using high-resolution magnetic resonance mapping

Mustapha Bouhrara, Luis E. Cortina, Abinand C. Rejimon, Nikkita Khattar, Christopher Bergeron, Janet Bergeron, Denise Melvin, Linda Zukley, Richard G. Spencer
2019 NeuroImage  
In this cross-sectional investigation, we studied a large cohort (n = 125) of cognitively unimpaired participants spanning a wide age range (21-94 years) and found a decrease in myelination with age in  ...  These studies have largely focused on the cerebrum, with very few MR investigations addressing age-dependent differences in the brainstem, in spite of its central role in the regulation of vital functions  ...  same atlas corresponding to the substantia nigra, red nucleus, and subthalamic nucleus.  ... 
doi:10.1016/j.neuroimage.2019.116307 pmid:31669302 pmcid:PMC6981041 fatcat:rtnryrpbmbah5lp3hy45e5gsuq

Quantitative whole-brain 3D imaging of tyrosine hydroxylase-labelled neuron architecture in the mouse MPTP model of Parkinson's disease

Urmas Roostalu, Casper B. G. Salinas, Ditte D. Thorbek, Jacob L. Skytte, Katrine Fabricius, Pernille Barkholt, Linu M. John, Vanessa Isabell Jurtz, Lotte Bjerre Knudsen, Jacob Jelsing, Niels Vrang, Henrik H. Hansen (+1 others)
2019 Disease Models & Mechanisms  
Also, MPTP dosing reduced overall TH signal intensity in basal ganglia nuclei, i.e. the substantia nigra, caudate-putamen, globus pallidus and subthalamic nucleus.  ...  Compared to vehicle controls, MPTP-dosed mice showed a significant loss of TH-positive neurons in the substantia nigra pars compacta and ventral tegmental area.  ...  ACKNOWLEDGEMENTS The authors would like to acknowledge Malene A. Christiansen and Nanna Windfeldt for skillful technical assistance.  ... 
doi:10.1242/dmm.042200 pmid:31704726 pmcid:PMC6899010 fatcat:jabg6gekyrfh7bklwqjdh64qqa

Multi-atlas tool for automated segmentation of brain gray matter nuclei and quantification of their magnetic susceptibility

Xu Li, Lin Chen, Kwame Kutten, Can Ceritoglu, Yue Li, Ningdong Kang, John Hsu, Ye Qiao, Hongjiang Wei, Chunlei Liu, Michael Miller, Susumu Mori (+3 others)
2019 NeuroImage  
internal/external, thalamus, pulvinar, subthalamic nucleus, substantia nigra, red nucleus and dentate nucleus in both left and right hemispheres.  ...  In summary, we designed a susceptibility multi-atlas tool for automated and reliable segmentation of QSM images and for quantification of magnetic susceptibilities.  ...  Acknowledgement The authors would like to thank Mr. Joseph Gillen, Ms. Terri Brawner, Ms. Kathleen Kahl, Ms. Ivana Kusevic, Dr. Li Pan for their assistance with data acquisition.  ... 
doi:10.1016/j.neuroimage.2019.02.016 pmid:30738207 pmcid:PMC6464637 fatcat:jn4mkiktlfet5pyk6rov3ndcte

Ultra-High 7T MRI of Structural Age-Related Changes of the Subthalamic Nucleus

M. C. Keuken, P.-L. Bazin, A. Schafer, J. Neumann, R. Turner, B. U. Forstmann
2013 Journal of Neuroscience  
In the present study, ultra-high field 7 tesla (T) magnetic resonance imaging (MRI) in humans was used to visualize and segment the STh in young, middle-aged, and elderly participants.  ...  In sum, the results of the present study suggest that age has to be taken into account in atlases for the optimal localization of the STh in healthy and diseased brains.  ...  Due to its small size and close proximity to structures such as the substantia nigra and the red nucleus, it has been a challenge to localize and visualize the STh (Mai and Paxinos, 2008 ).  ... 
doi:10.1523/jneurosci.3241-12.2013 pmid:23486960 pmcid:PMC6619019 fatcat:libprr7kv5atvcb2ouhrif5pnm

High-resolution characterisation of the aging brain using simultaneous quantitative susceptibility mapping (QSM) and R 2 * measurements at 7 T

Matthew J. Betts, Julio Acosta-Cabronero, Arturo Cardenas-Blanco, Peter J. Nestor, Emrah Düzel
2016 NeuroImage  
Within the basal ganglia system-but also hippocampus and cerebellar dentate nucleus-, QSM was largely in agreement with R2* with the exception of the globus pallidus.  ...  We asked which of the two techniques would be more sensitive to explore global differences in tissue composition in elderly adults relative to young subjects.  ...  In (B), the internal globus pallidus (GPi; brown), external globus pallidus (GPe; pink), dentate nucleus (DN; green) subthalamic nucleus (STN; red), substantia nigra (SN; blue) and red nucleus (yellow)  ... 
doi:10.1016/j.neuroimage.2016.05.024 pmid:27181761 fatcat:fupj23xazjbl7kmqkzzwkz2a4m

Validation of MRI-based 3D digital atlas registration with histological and autoradiographic volumes: An anatomofunctional transgenic mouse brain imaging study

J. Lebenberg, A.-S. Hérard, A. Dubois, J. Dauguet, V. Frouin, M. Dhenain, P. Hantraye, T. Delzescaux
2010 NeuroImage  
To accurately study neuroanatomy and brain function in small animals, histological staining and ex vivo autoradiography remain the gold standards to date.  ...  We therefore proposed to match a 3D digital atlas with previously 3D-reconstructed post mortem data in order to automatically evaluate morphology and function in mouse brain structures.  ...  Acknowledgments We thank the Sanofi-Aventis Neurodegenerative Disease Group for providing the transgenic mice involved in this study.  ... 
doi:10.1016/j.neuroimage.2010.03.014 pmid:20226256 fatcat:vckoy23eivflrmrvkllhxa3tim

Quantitative Susceptibility Mapping: Contrast Mechanisms and Clinical Applications

2015 Tomography  
It first uses the frequency shift in the MRI signal to map the magnetic field profile within the tissue.  ...  More importantly, magnetic susceptibility directly reflects the molecular composition and cellular architecture of the tissue.  ...  pallidus, substantia nigra, red nucleus, caudate nucleus and putamen, and thalamus.  ... 
doi:10.18383/j.tom.2015.00136 pmid:26844301 pmcid:PMC4734903 fatcat:asrfxxhhcrbpnobdc3hjkhnlfq

Neuroimaging at 7 Tesla: a pictorial narrative review

Tomohisa Okada, Koji Fujimoto, Yasutaka Fushimi, Thai Akasaka, Dinh H. D. Thuy, Atsushi Shima, Nobukatsu Sawamoto, Naoya Oishi, Zhilin Zhang, Takeshi Funaki, Yuji Nakamoto, Toshiya Murai (+3 others)
2021 Quantitative Imaging in Medicine and Surgery  
pallidus, thalamus and substantia nigra, and in small structures, such as the subthalamic nucleus, habenula, perforating arteries, and the perivascular space, that are difficult to observe at lower magnetic  ...  Neuroimaging using the 7-Tesla (7T) human magnetic resonance (MR) system is rapidly gaining popularity after being approved for clinical use in the European Union and the USA.  ...  Surface maps show the average of 22 young (20-30 years old) and 8 aged (>60 years old) subjects. Decreases in cortical thickness and increases in R1 values are observed by aging.  ... 
doi:10.21037/qims-21-969 pmid:35655840 pmcid:PMC9131333 fatcat:oqsv2jjohbcx7ojaub5bikc6ce

Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T

Elena Najdenovska, Constantin Tuleasca, João Jorge, Philippe Maeder, José P. Marques, Timo Roine, Daniel Gallichan, Jean-Philippe Thiran, Marc Levivier, Meritxell Bach Cuadra
2019 Scientific Reports  
Our work aims to assess the distinguishable Vim on 7 T SWI in both healthy-population and patients and, using it as a reference, to compare it with: (1) The clinical targeting, (2) The automated parcellation  ...  of thalamic subparts based on 3 T diffusion MRI (dMRI), and (3) The multi-atlas segmentation techniques.  ...  Institute of Technology Lausanne (EPFL), the University of Geneva (UniGe), the Centre Hospitalier Universitaire Vaudois (CHUV), the Hôpitaux Universitaires de Genève (HUG), and the Leenaards and Jeantet  ... 
doi:10.1038/s41598-018-37825-8 pmid:30718634 pmcid:PMC6361927 fatcat:ypjhcm33kba5foaj44br2boyhi

Multi-contrast anatomical subcortical structures parcellation

Pierre-Louis Bazin, Anneke Alkemade, Martijn J Mulder, Amanda G Henry, Birte U Forstmann
2020 eLife  
The human subcortex is comprised of more than 450 individual nuclei which lie deep in the brain.  ...  The new algorithm has been tested on 17 prominent subcortical structures based on a large quantitative MRI dataset at 7 Tesla.  ...  Automated segmentation of the Substantia Nigra, subthalamic nucleus and red nucleus in 7T data at young and old age NeuroImage 139 :324–336.  ... 
doi:10.7554/elife.59430 fatcat:64xrswbhyzce5frfmbl4g5t5qu

Regional Infant Brain Development: An MRI-Based Morphometric Analysis in 3 to 13 Month Olds

M.-s. Choe, S. Ortiz-Mantilla, N. Makris, M. Gregas, J. Bacic, D. Haehn, D. Kennedy, R. Pienaar, V. S. Caviness, A. A. Benasich, P. E. Grant
2012 Cerebral Cortex  
gradient echo images and detailed semi-automated brain segmentation.  ...  Here we report global and regional volumetric growth of cerebrum, cerebellum, and brainstem with gender dimorphism, in 33 cross-sectional scans, over 3 to 13 months, using T 1 -weighted 3-dimensional spoiled  ...  This area includes the hypothalamus, mammillary body, subthalamic nuclei, substantia nigra, red nucleus, lateral geniculate nucleus, and medial geniculate nucleus.  ... 
doi:10.1093/cercor/bhs197 pmid:22772652 pmcid:PMC3729199 fatcat:gjgb3uq6yvf7toyse42dxfy5ae

The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease

Alexandra Badea, Lauren Kane, Robert J. Anderson, Yi Qi, Mark Foster, Gary P. Cofer, Neil Medvitz, Anne F. Buckley, Andreas K. Badea, William C. Wetsel, Carol A. Colton
2016 NeuroImage  
Graphical Abstract One line summary White matter changes in the fimbria/fornix play a role in the progression of AD, and can be used as a biomarker of disease, and as a target for therapy Keywords Alzheimer's  ...  The demonstration of white matter abnormalities in the CVN-AD mouse model, in tracts relevant to AD, would support that changes in white matter have an important role in AD, and potential predictive value  ...  The Center for In Vivo Microscopy is supported through NIH awards P41 EB015897 and 1S10OD010683-01 (to Dr. G Allan Johnson).  ... 
doi:10.1016/j.neuroimage.2016.08.014 pmid:27521741 pmcid:PMC5159324 fatcat:n3tleh6cczcalkhj5qwfz463ga
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