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https://www.readbyqxmd.com/read/28188873/an-improved-fsl-first-pipeline-for-subcortical-gray-matter-segmentation-to-study-abnormal-brain-anatomy-using-quantitative-susceptibility-mapping-qsm
#1
Xiang Feng, Andreas Deistung, Michael G Dwyer, Jesper Hagemeier, Paul Polak, Jessica Lebenberg, Frédérique Frouin, Robert Zivadinov, Jürgen R Reichenbach, Ferdinand Schweser
Accurate and robust segmentation of subcortical gray matter (SGM) nuclei is required in many neuroimaging applications. FMRIB's Integrated Registration and Segmentation Tool (FIRST) is one of the most popular software tools for automated subcortical segmentation based on T1-weighted (T1w) images. In this work, we demonstrate that FIRST tends to produce inaccurate SGM segmentation results in the case of abnormal brain anatomy, such as present in atrophied brains, due to a poor spatial match of the subcortical structures with the training data in the MNI space as well as due to insufficient contrast of SGM structures on T1w images...
February 7, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28168364/effects-of-aging-on-formula-see-text-formula-see-text-and-qsm-mri-values-in-the-subcortex
#2
M C Keuken, P-L Bazin, K Backhouse, S Beekhuizen, L Himmer, A Kandola, J J Lafeber, L Prochazkova, A Trutti, A Schäfer, R Turner, B U Forstmann
The aging brain undergoes several anatomical changes that can be measured with Magnetic Resonance Imaging (MRI). Early studies using lower field strengths have assessed changes in tissue properties mainly qualitatively, using [Formula: see text]- or [Formula: see text]- weighted images to provide image contrast. With the development of higher field strengths (7 T and above) and more advanced MRI contrasts, quantitative measures can be acquired even of small subcortical structures. This study investigates volumetric, spatial, and quantitative MRI parameter changes associated with healthy aging in a range of subcortical nuclei, including the basal ganglia, red nucleus, and the periaqueductal grey...
February 6, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/28126551/exploring-the-origins-of-echo-time-dependent-quantitative-susceptibility-mapping-qsm-measurements-in-healthy-tissue-and-cerebral-microbleeds
#3
Matthew J Cronin, Nian Wang, Kyle S Decker, Hongjiang Wei, Wen-Zhen Zhu, Chunlei Liu
Quantitative susceptibility mapping (QSM) is increasingly used to measure variation in tissue composition both in the brain and in other areas of the body in a range of disease pathologies. Although QSM measurements were originally believed to be independent of the echo time (TE) used in the gradient-recalled echo (GRE) acquisition from which they are derived; recent literature (Sood et al., 2016) has shown that these measurements can be highly TE-dependent in a number of brain regions. In this work we systematically investigate possible causes of this effect through analysis of apparent frequency and QSM measurements derived from data acquired at multiple TEs in vivo in healthy brain regions and in cerebral microbleeds (CMBs); QSM data acquired in a gadolinium-doped phantom; and in QSM data derived from idealized simulated phase data...
January 23, 2017: NeuroImage
https://www.readbyqxmd.com/read/28113841/quantitative-susceptibility-mapping-using-structural-feature-based-collaborative-reconstruction-sfcr-in-the-human-brain
#4
Lijun Bao, Xu Li, Congbo Cai, Zhong Chen, Peter van Zijl
The reconstruction of MR quantitative susceptibility mapping (QSM) from local phase measurements is an ill posed inverse problem and different regularization strategies incorporating a priori information extracted from magnitude and phase images have been proposed. However, the anatomy observed in magnitude and phase images does not always coincide spatially with that in susceptibility maps, which could give erroneous estimation in the reconstructed susceptibility map. In this paper, we develop a structural feature based collaborative reconstruction (SFCR) method for QSM including both magnitude and susceptibility based information...
March 22, 2016: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28113561/implementing-nonlinear-feedback-controllers-using-dna-strand-displacement-reactions
#5
Rucha Sawlekar, Francesco Montefusco, Vishwesh V Kulkarni, Declan G Bates
We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration...
April 29, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28097689/investigating-magnetic-susceptibility-of-human-knee-joint-at-7-tesla
#6
Hongjiang Wei, Russell Dibb, Kyle Decker, Nian Wang, Yuyao Zhang, Xiaopeng Zong, Weili Lin, Daniel B Nissman, Chunlei Liu
PURPOSE: To evaluate the magnetic susceptibility properties of different anatomical structures within the knee joint using quantitative susceptibility mapping (QSM). METHODS: A collagen tissue model was simulated and ex vivo animal cartilage experiments were conducted at 9.4 Tesla (T) to evaluate the B0 orientation-dependent magnetic susceptibility contrast observed in cartilage. Furthermore, nine volunteers (six healthy subjects without knee pain history and three patients with known knee injury, between 29 and 58 years old) were scanned using gradient-echo acquisitions on a high-field 7T MR scanner...
January 17, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28065850/deep-grey-matter-iron-accumulation-in-alcohol-use-disorder
#7
Michal Juhás, Hongfu Sun, Matthew R G Brown, Marnie B MacKay, Karl F Mann, Wolfgang H Sommer, Alan H Wilman, Serdar M Dursun, Andrew J Greenshaw
PURPOSE: Evaluate brain iron accumulation in alcohol use disorder (AUD) patients compared to controls using quantitative susceptibility mapping (QSM). METHODS: QSM was performed retrospectively by using phase images from resting state functional magnetic resonance imaging (fMRI). 20 male AUD patients and 15 matched healthy controls were examined. Susceptibility values were manually traced in deep grey matter regions including caudate nucleus, combined putamen and globus pallidus, combined substantia nigra and red nucleus, dentate nucleus, and a reference white matter region in the internal capsule...
January 5, 2017: NeuroImage
https://www.readbyqxmd.com/read/28046752/su-f-i-24-feasibility-of-magnetic-susceptibility-to-relative-electron-density-conversion-method-for-radiation-therapy
#8
K Ito, N Kadoya, M Chiba, K Sato, T Nagasaka, K Yamanaka, S Dobashi, K Takeda, H Matsushita, K Jingu
PURPOSE: The aim of this study is to develop radiation treatment planning using magnetic susceptibility obtained from quantitative susceptibility mapping (QSM) via MR imaging. This study demonstrates the feasibility of a method for generating a substitute for a CT image from an MRI. METHODS: The head of a healthy volunteer was scanned using a CT scanner and a 3.0 T MRI scanner. The CT imaging was performed with a slice thickness of 2.5 mm at 80 and 120 kV (dual-energy scan)...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046245/su-d-207a-04-use-of-gradient-echo-plural-contrast-imaging-gepci-in-mr-guided-radiation-therapy-a-feasibility-study-targeting-brain-treatment
#9
B Cai, J Wen, Y Rao, C Tsien, J Huang, O Green, S Mutic, D Yablonskiy, H Gach
PURPOSE: To implement the Gradient Echo Plural Contrast Imaging(GEPCI) technique in MRI-simulation for radiation therapy and assess the feasibility of using GEPCI images with advanced inhomogeneity correction in MRI-guided radiotherapy for brain treatment. METHODS: An optimized multigradient-echo GRE sequence (TR=50ms;TE1=4ms;delta_TE=4ms;flip angle=300,11 Echoes) was developed to generate both structural (T1w and T2*w) and functional MRIs (field and susceptibility maps) from a single acquisition...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/27995062/magnetic-susceptibility-in-the-deep-layers-of-the-primary-motor-cortex-in-amyotrophic-lateral-sclerosis
#10
M Costagli, G Donatelli, L Biagi, E Caldarazzo Ienco, G Siciliano, M Tosetti, M Cosottini
Amyotrophic Lateral Sclerosis (ALS) is a progressive neurological disorder that entails degeneration of both upper and lower motor neurons. The primary motor cortex (M1) in patients with upper motor neuron (UMN) impairment is pronouncedly hypointense in Magnetic Resonance (MR) T2* contrast. In the present study, 3D gradient-recalled multi-echo sequences were used on a 7 Tesla MR system to acquire T2*-weighted images targeting M1 at high spatial resolution. MR raw data were used for Quantitative Susceptibility Mapping (QSM)...
2016: NeuroImage: Clinical
https://www.readbyqxmd.com/read/27987234/deciphering-fungal-dimorphism-farnesol-s-unanswered-questions
#11
Kenneth W Nickerson, Audrey L Atkin
Candida albicans excretes E,E-farnesol as a virulence factor and quorum sensing molecule that prevents the yeast to hyphal conversion. Polke et al. (2016) identified eed1Δ/Δ as the first farnesol hypersensitive mutant of C. albicans. eed1Δ/Δ also excretes 10X more farnesol and while able to form hyphae, it cannot maintain hyphae. This mutant enables new research into unanswered questions, including the existence of potential farnesol receptors and transporters, regulation of farnesol synthesis, and relationships among farnesol, germ tube formation and hyphal maintenance...
December 17, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27986608/changes-in-brain-iron-concentration-after-exposure-to-high-altitude-hypoxia-measured-by-quantitative-susceptibility-mapping
#12
Lin Chen, Congbo Cai, Tianhe Yang, Jianzhong Lin, Shuhui Cai, Jiaxing Zhang, Zhong Chen
Hypoxia can induce physiological changes. This study aims to explore effects of high-altitude (HA) hypoxia on cerebral iron concentration. Twenty-nine healthy sea-level participants were tested shortly before and after approximately 4-week adaptation to the HA environment at fQinghai-Tibet Plateau (4200m), and were re-investigated after re-adaptation to the sea-level environment one year later. Iron concentration was quantified with quantitative susceptibility mapping (QSM), and the results were compared with transverse relaxation rate (R(*)2) measurements...
February 15, 2017: NeuroImage
https://www.readbyqxmd.com/read/27939794/studying-cyto-and-myeloarchitecture-of-the-human-cortex-at-ultra-high-field-with-quantitative-imaging-r1-r2-and-magnetic-susceptibility
#13
José P Marques, Diana Khabipova, Rolf Gruetter
In this manuscript, the use of quantitative imaging at ultra-high field is evaluated as a mean to study cyto and myelo-architecture of the cortex. The quantitative contrasts used are the longitudinal relaxation rate (R1), apparent transverse relaxation rate (R2(*)) and quantitative susceptibility mapping (QSM). The quantitative contrasts were computed using high resolution in-vivo (0.65mm isotropic) brain data acquired at 7T. The performance of the different quantitative approaches was evaluated by visualizing the contrast between known highly myelinated primary sensory cortex regions and the neighbouring cortex...
February 15, 2017: NeuroImage
https://www.readbyqxmd.com/read/27906525/the-clinical-utility-of-qsm-disease-diagnosis-medical-management-and-surgical-planning
#14
REVIEW
Sarah Eskreis-Winkler, Yan Zhang, Jingwei Zhang, Zhe Liu, Alexey Dimov, Ajay Gupta, Yi Wang
Quantitative susceptibility mapping (QSM) is an MR technique that depicts and quantifies magnetic susceptibility sources. Mapping iron, the dominant susceptibility source in the brain, has many important clinical applications. Herein, we review QSM applications in the diagnosis, medical management, and surgical treatment of disease. To assist in early disease diagnosis, QSM can identify elevated iron levels in the motor cortex of amyotrophic lateral sclerosis patients, in the substantia nigra of Parkinson's disease (PD) patients, in the globus pallidus, putamen, and caudate of Huntington's disease patients, and in the basal ganglia of Wilson's disease patients...
December 1, 2016: NMR in Biomedicine
https://www.readbyqxmd.com/read/27859983/imaging-of-nigrosome-1-in-substantia-nigra-at-3t-using-multiecho-susceptibility-map-weighted-imaging-smwi
#15
Yoonho Nam, Sung-Min Gho, Dong-Hyun Kim, Eung Yeop Kim, Jongho Lee
PURPOSE: To enhance the visibility of nigrosome 1 in substantia nigra, which has recently been suggested as an imaging biomarker for Parkinson's disease (PD) at 3T magnetic resonance imaging (MRI). MATERIALS AND METHODS: The substantia nigra structure was visualized at 3T MRI using multiecho susceptibility map-weighted imaging (SMWI) in 15 healthy volunteers and 6 patients with Parkinson's disease (PD). The visibility of nigrosome 1 was further enhanced by acquiring data in an oblique-coronal imaging plane at a high spatial resolution (0...
November 11, 2016: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/27833539/validity-of-quinpirole-sensitization-rat-model-of-ocd-linking-evidence-from-animal-and-clinical-studies
#16
REVIEW
Ales Stuchlik, Dominika Radostová, Hana Hatalova, Karel Vales, Tereza Nekovarova, Jana Koprivova, Jan Svoboda, Jiri Horacek
Obsessive-compulsive disorder (OCD) is a neuropsychiatric disorder with 1-3% prevalence. OCD is characterized by recurrent thoughts (obsessions) and repetitive behaviors (compulsions). The pathophysiology of OCD remains unclear, stressing the importance of pre-clinical studies. The aim of this article is to critically review a proposed animal model of OCD that is characterized by the induction of compulsive checking and behavioral sensitization to the D2/D3 dopamine agonist quinpirole. Changes in this model have been reported at the level of brain structures, neurotransmitter systems and other neurophysiological aspects...
2016: Frontiers in Behavioral Neuroscience
https://www.readbyqxmd.com/read/27821737/quasimodo-mediates-daily-and-acute-light-effects-on-drosophila-clock-neuron-excitability
#17
Edgar Buhl, Adam Bradlaugh, Maite Ogueta, Ko-Fan Chen, Ralf Stanewsky, James J L Hodge
We have characterized a light-input pathway regulating Drosophila clock neuron excitability. The molecular clock drives rhythmic electrical excitability of clock neurons, and we show that the recently discovered light-input factor Quasimodo (Qsm) regulates this variation, presumably via an Na(+), K(+), Cl(-) cotransporter (NKCC) and the Shaw K(+) channel (dKV3.1). Because of light-dependent degradation of the clock protein Timeless (Tim), constant illumination (LL) leads to a breakdown of molecular and behavioral rhythms...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27763692/accelerated-mapping-of-magnetic-susceptibility-using-3d-planes-on-a-paddlewheel-pop-epi-at-ultra-high-field-strength
#18
Daniel Stäb, Steffen Bollmann, Christian Langkammer, Kristian Bredies, Markus Barth
With the advent of ultra-high field MRI scanners in clinical research, susceptibility based MRI has recently gained increasing interest because of its potential to assess subtle tissue changes underlying neurological pathologies/disorders. Conventional, but rather slow, three-dimensional (3D) spoiled gradient-echo (GRE) sequences are typically employed to assess the susceptibility of tissue. 3D echo-planar imaging (EPI) represents a fast alternative but generally comes with echo-time restrictions, geometrical distortions and signal dropouts that can become severe at ultra-high fields...
October 20, 2016: NMR in Biomedicine
https://www.readbyqxmd.com/read/27748454/colocalization-of-cerebral-iron-with-amyloid-beta-in-mild-cognitive-impairment
#19
J M G van Bergen, X Li, J Hua, S J Schreiner, S C Steininger, F C Quevenco, M Wyss, A F Gietl, V Treyer, S E Leh, F Buck, R M Nitsch, K P Pruessmann, P C M van Zijl, C Hock, P G Unschuld
Quantitative Susceptibility Mapping (QSM) MRI at 7 Tesla and 11-Carbon Pittsburgh-Compound-B PET were used for investigating the relationship between brain iron and Amyloid beta (Aβ) plaque-load in a context of increased risk for Alzheimer's disease (AD), as reflected by the Apolipoprotein E ε4 (APOE-e4) allele and mild cognitive impairment (MCI) in elderly subjects. Carriers of APOE-e4 with normal cognition had higher cortical Aβ-plaque-load than non-carriers. In MCI an association between APOE-e4 and higher Aβ-plaque-load was observable both for cortical and subcortical brain-regions...
October 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27744181/rapid-reconstruction-of-quantitative-susceptibility-mapping-via-improved-%C3%A2-0-norm-approximation
#20
Congbo Cai, Xi Chen, Weijun Liu, Shuhui Cai, Delu Zeng, Xinghao Ding
Quantitative susceptibility mapping (QSM) reconstruction is a well-known ill-posed problem. Various regularization techniques have been proposed for solving this problem. In this paper, a rapid method is proposed that uses ℓ0 norm minimization in a gradient domain. Because ℓ0 minimization is an NP-hard problem, a special alternating optimization strategy is employed to simplify the reconstruction algorithm. The proposed algorithm uses only simple point-wise multiplications and thresholding operations, and significantly speeds up the calculation...
October 4, 2016: Computers in Biology and Medicine
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