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Benning M.,Magnetic Resonance Research Center | Gladden L.,Magnetic Resonance Research Center | Holland D.,Magnetic Resonance Research Center | Schonlieb C.-B.,University of Cambridge | And 3 more authors.
Journal of Magnetic Resonance | Year: 2014

In recent years there has been significant developments in the reconstruction of magnetic resonance velocity images from sub-sampled k-space data. While showing a strong improvement in reconstruction quality compared to classical approaches, the vast number of different methods, and the challenges in setting them up, often leaves the user with the difficult task of choosing the correct approach, or more importantly, not selecting a poor approach. In this paper, we survey variational approaches for the reconstruction of phase-encoded magnetic resonance velocity images from sub-sampled k-space data. We are particularly interested in regularisers that correctly treat both smooth and geometric features of the image. These features are common to velocity imaging, where the flow field will be smooth but interfaces between the fluid and surrounding material will be sharp, but are challenging to represent sparsely. As an example we demonstrate the variational approaches on velocity imaging of water flowing through a packed bed of solid particles. We evaluate Wavelet regularisation against Total Variation and the relatively recent second order Total Generalised Variation regularisation. We combine these regularisation schemes with a contrast enhancement approach called Bregman iteration. We verify for a variety of sampling patterns that Morozov's discrepancy principle provides a good criterion for stopping the iterations. Therefore, given only the noise level, we present a robust guideline for setting up a variational reconstruction scheme for MR velocity imaging. © 2013 Elsevier Inc. All rights reserved.


Amin S.A.,Magnetic Resonance Research Center | Leinenweber K.,Arizona State University | Benmore C.J.,Argonne National Laboratory | Weber R.,Argonne National Laboratory | And 2 more authors.
Journal of Physical Chemistry C | Year: 2012

27Al NMR is used to quantify coordination changes in CaAl 2O 4 glass pressure cycled to 16 GPa. The structure and coordination environments remain unchanged up to 8 GPa, at which 93% of the recovered glass exists as four-fold Al, whereas the remaining population exists as [5,6]Al. Upon densification, [5,6]Al comprises nearly 30% of observed Al, most likely through the generation of three-coordinated oxygen. Negligible changes are observed for the isotropic chemical shift ( [4]Al ? 78.8 ppm, [5]Al ? 46.3 ppm, [6]Al ? 12.6 ppm) and average quadrupole coupling strengths with pressure. 3QMAS spectra suggest less distortion within the newly formed Al environments in comparison with [4]Al. The chemical shift of [4]Al suggests that the aluminate network remains fully polymerized in glasses quenched from pressures up to 16 GPa. © 2011 American Chemical Society.


Scheinost D.,Yale University | Scheinost D.,Magnetic Resonance Research Center | Hampson M.,Yale University | Qiu M.,Yale University | And 3 more authors.
Neuroinformatics | Year: 2013

Real-time functional magnetic resonance imaging (rt-fMRI) has recently gained interest as a possible means to facilitate the learning of certain behaviors. However, rt-fMRI is limited by processing speed and available software, and continued development is needed for rt-fMRI to progress further and become feasible for clinical use. In this work, we present an open-source rt-fMRI system for biofeedback powered by a novel Graphics Processing Unit (GPU) accelerated motion correction strategy as part of the BioImage Suite project (www.bioimagesuite.org). Our system contributes to the development of rt-fMRI by presenting a motion correction algorithm that provides an estimate of motion with essentially no processing delay as well as a modular rt-fMRI system design. Using empirical data from rt-fMRI scans, we assessed the quality of motion correction in this new system. The present algorithm performed comparably to standard (non real-time) offline methods and outperformed other real-time methods based on zero order interpolation of motion parameters. The modular approach to the rt-fMRI system allows the system to be flexible to the experiment and feedback design, a valuable feature for many applications. We illustrate the flexibility of the system by describing several of our ongoing studies. Our hope is that continuing development of open-source rt-fMRI algorithms and software will make this new technology more accessible and adaptable, and will thereby accelerate its application in the clinical and cognitive neurosciences. © 2013 Springer Science+Business Media New York.


Rothman D.L.,Yale University | De Feyter H.M.,Yale University | Maciejewski P.K.,Harvard University | Behar K.L.,Magnetic Resonance Research Center
Neurochemical Research | Year: 2012

The high in vivo flux of the glutamate/glutamine cycle puts a strong demand on the return of ammonia released by phosphate activated glutaminase from the neurons to the astrocytes in order to maintain nitrogen balance. In this paper we review several amino acid shuttles that have been proposed for balancing the nitrogen flows between neurons and astrocytes in the glutamate/glutamine cycle. All of these cycles depend on the directionality of glutamate dehydrogenase, catalyzing reductive glutamate synthesis (forward reaction) in the neuron in order to capture the ammonia released by phosphate activated glutaminase, while catalyzing oxidative deamination of glutamate (reverse reaction) in the astrocytes to release ammonia for glutamine synthesis. Reanalysis of results from in vivo experiments using 13N and 15N labeled ammonia and 15N leucine in rats suggests that the maximum flux of the alanine/ lactate or branched chain amino acid/branched chain amino acid transaminase shuttles between neurons and astrocytes are approximately 3-5 times lower than would be required to account for the ammonia transfer from neurons to astrocytes needed for glutamine synthesis (amide nitrogen) to sustain the glutamate/glutamine cycle. However, in the rat brain both the total ammonia fixation rate by glutamate dehydrogenase and the total branched chain amino acid transaminase activity are sufficient to support a branched chain amino acid/branched chain keto acid shuttle, as proposed by Hutson and coworkers, which would support the de novo synthesis of glutamine in the astrocyte to replace the 20 % of neurotransmitter glutamate that is oxidized. A higher fraction of the nitrogen needs of total glutamate neurotransmitter cycling could be supported by hybrid cycles in which glutamate and tricarboxylic acid cycle intermediates act as a nitrogen shuttle. A limitation of all in vivo studies in animals conducted to date is that none have shown transfer of nitrogen for glutamine amide synthesis, either as free ammonia or via an amino acid from the neurons to the astrocytes. Future work will be needed, perhaps using methods for selectively labeling nitrogen in neurons, to conclusively establish the rate of amino acid nitrogen shuttles in vivo and their coupling to the glutamate/glutamine cycle. © Springer Science+Business Media New York 2012.


Madden D.C.,University of Cambridge | Bentley M.L.,University of Cambridge | Bentley M.L.,Magnetic Resonance Research Center | Jenkins S.J.,University of Cambridge | Driver S.M.,University of Cambridge
Surface Science | Year: 2014

We have compared the behaviour of enantiopure alanine, racemic alanine and glycine on Cu{311} surfaces, using LEED and STM to elucidate the self-organisation. In most respects, similar behaviour is seen in all three cases. At 0.33 ML, an overlayer with (2,1;1,2) periodicity is seen: the "symmetric lattice" (SL) phase. The adsorbate, in anionic form (alaninate or glycinate), adopts a 3-point (μ3) bonding configuration. At higher coverages, networks of boundaries emerge whose orientations break the substrate mirror symmetry. The boundary structure is locally chiral. This "chiral lattice" (CL) phase involves mixed 2-point (μ2) and μ3 bonding. The CL phase reverts to the SL phase on annealing above 430-440 K. That glycinate forms chiral boundaries demonstrates that boundary chirality can occur without molecular chirality. Glycinate boundaries are very short (10-20 Å), and occur in both enantiomeric forms. Enantiopure alaninate boundaries are much longer (several hundred Å), occurring exclusively in one enantiomeric form which is tied to the molecular enantiomer used. Racemic alaninate overlayers exhibit l-alaninate-like domains alternating with d-alaninate-like domains over a length scale of the order of 100 Å. The principal influence of the methyl group, where present, is therefore on which boundary enantiomer occurs, and on the boundary lengths. © 2014 Elsevier B.V.


PubMed | University of Cambridge and Magnetic Resonance Research Center
Type: | Journal: Journal of magnetic resonance (San Diego, Calif. : 1997) | Year: 2014

In recent years there has been significant developments in the reconstruction of magnetic resonance velocity images from sub-sampled k-space data. While showing a strong improvement in reconstruction quality compared to classical approaches, the vast number of different methods, and the challenges in setting them up, often leaves the user with the difficult task of choosing the correct approach, or more importantly, not selecting a poor approach. In this paper, we survey variational approaches for the reconstruction of phase-encoded magnetic resonance velocity images from sub-sampled k-space data. We are particularly interested in regularisers that correctly treat both smooth and geometric features of the image. These features are common to velocity imaging, where the flow field will be smooth but interfaces between the fluid and surrounding material will be sharp, but are challenging to represent sparsely. As an example we demonstrate the variational approaches on velocity imaging of water flowing through a packed bed of solid particles. We evaluate Wavelet regularisation against Total Variation and the relatively recent second order Total Generalised Variation regularisation. We combine these regularisation schemes with a contrast enhancement approach called Bregman iteration. We verify for a variety of sampling patterns that Morozovs discrepancy principle provides a good criterion for stopping the iterations. Therefore, given only the noise level, we present a robust guideline for setting up a variational reconstruction scheme for MR velocity imaging.

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