Robust automated shimming technique using arbitrary mapping acquisition parameters (RASTAMAP)

Klassen, L. Martyn; Menon, Ravi S.

doi:10.1002/mrm.20094

Cited by 84 publications

(69 citation statements)

References 22 publications

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“…Imaging was performed on a 9.4 T, 31-cm horizontal-bore animal MRI scanner (Agilent Technologies). An in-house-designed B 0 field mapping sequence, robust automated shimming technique using arbitrary acquisition parameters (RASTAMAP) (26), was used to perform automated higher-order shimming before imaging. The rf coil used for all data collection was a 4-cm-diameter millipede coil (Agilent Technologies).…”

Section: Methodsmentioning

confidence: 99%

Origins of R ₂ ^∗ orientation dependence in gray and white matter

Rudko

Klassen²,

Chickera³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Estimates of the apparent transverse relaxation rate (R 2 * ) can be used to quantify important properties of biological tissue. Surprisingly, the mechanism of R 2 * dependence on tissue orientation is not well understood. The primary goal of this paper was to characterize orientation dependence of R 2 * in gray and white matter and relate it to independent measurements of two other susceptibility based parameters: the local Larmor frequency shift (f L ) and quantitative volume magnetic susceptibility (Δχ ). Through this comparative analysis we calculated scaling relations quantifying R 2 ′ (reversible contribution to the transverse relaxation rate from local field inhomogeneities) in a voxel given measurements of the local Larmor frequency shift. R 2 ′ is a measure of both perturber geometry and density and is related to tissue microstructure. Additionally, two methods (the Generalized Lorentzian model and iterative dipole inversion) for calculating Δχ were compared in gray and white matter. The value of Δχ derived from fitting the Generalized Lorentzian model was then connected to the observed R 2 * orientation dependence using image-registered optical density measurements from histochemical staining. Our results demonstrate that the R 2 * and f L of white and cortical gray matter are well described by a sinusoidal dependence on the orientation of the tissue and a linear dependence on the volume fraction of myelin in the tissue. In deep brain gray matter structures, where there is no obvious symmetry axis, R 2 * and f L have no orientation dependence but retain a linear dependence on tissue iron concentration and hence Δχ .MRI contrast mechanisms | grey matter | cellular architecture | relaxation times I n many neurological diseases such as multiple sclerosis, Alzheimer's, and Parkinson, and in conditions following traumatic brain injury, microstructural changes occur in gray and white matter (1-4). One method for quantifying these microstructural changes is the mapping of the effective transverse relaxation rate (R p 2 ). Along with the longitudinal relaxation rate (R 1 ) and transverse relaxation rate (R 2 ), R p 2 has been viewed as a fundamental MRI tissue parameter, affected by several factors including myelin content (5, 6), endogenous ferritin-based (Fe 3+ ) iron (7,8), tissue microstructure (6), and paramagnetic, blood deoxyhemoglobin (9). However, a number of recent studies have reported a somewhat surprising dependence of R p 2 on tissue orientation, at least in white matter (10-12). The purpose of this paper was to investigate the mechanisms that could contribute to this orientation dependence of R p 2 in both gray and white matter. Because R p 2 is influenced by magnetic field perturbations, we examined the role of local Larmor frequency shift (f L ) and quantitative magnetic susceptibility (Δχ), parameters that relate field and frequency. Through this analysis we identified unique scaling relations that relate R 2 ′ to the local Larmor frequency shift calculated after removal of macroscopic field ...

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Section: Methodsmentioning

confidence: 99%

Origins of R ₂ ^∗ orientation dependence in gray and white matter

Rudko

Klassen²,

Chickera³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…An optimized home-built 1.5 ϫ 2.0 cm linear transmit-receive surface coil was positioned proximally to the anterior aspect of the rat's head for imaging. An automated shimming algorithm was used to optimize the magnetic field over our imaging volume of interest using RASTAMAP (Klassen and Menon 2004). Ten or 13 1-mm-thick coronal or horizontal slices covering the brain were selected.…”

Section: Mri Acquisitionmentioning

confidence: 99%

Functional Networks in the Anesthetized Rat Brain Revealed by Independent Component Analysis of Resting-State fMRI

Hutchison

Mirsattari

Jones

et al. 2010

Journal of Neurophysiology

149

143

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Hutchison RM, Mirsattari SM, Jones CK, Gati JS, Leung LS. Functional networks in the anesthetized rat brain revealed by independent component analysis of resting-state fMRI. J Neurophysiol 103: 3398-3406, 2010. First published April 21, 2010 doi:10.1152/jn.00141.2010. The rodent brain is organized into functional networks that can be studied through examination of synchronized low-frequency spontaneous fluctuations (LFFs) of the functional magnetic resonance imaging -blood-oxygen-level-dependent (BOLD) signal. In this study, resting networks of LFFs were estimated from the whole-brain BOLD signals using independent component analysis (ICA). ICA provides a hypothesis-free technique for determining the functional connectivity map that does not require a priori selection of a seed region. Twenty Long-Evans rats were anesthetized with isoflurane (1%, n ϭ 10) or ketamine/xylazine (50/6 mg · kg Ϫ1 · h Ϫ1 ip, n ϭ 10) and imaged for 5-10 min in a 9.4 T MR scanner without experimental stimulation or task requirement. Independent, synchronous LFFs of BOLD signals were found to exist in clustered, bilaterally symmetric regions of both cortical and subcortical structures, including primary and secondary somatosensory cortices, motor cortices, visual cortices, posterior and anterior cingulate cortices, hippocampi, caudate-putamen, and thalamic and hypothalamic nuclei. The somatosensory and motor cortices typically demonstrated both symmetric and asymmetric components with unique frequency profiles. Similar independent network components were found under isoflurane and ketamine/xylazine anesthesia. The report demonstrates, for the first time, 12 independent resting networks that are bilaterally synchronous in different cortical and subcortical areas of the rat brain.

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“…Slices were acquired at a 30°caudal tilt with respect to the anterior commissure to posterior commissure (ACPC) line (Damasio, 1995), covering occipital, parietal, posterior temporal and posterior frontal cortices. A constrained, three-dimensional phase shimming procedure was performed to optimize the magnetic field homogeneity over the prescribed functional planes (Klassen and Menon, 2004). Physiologic fluctuations were compensated for every segment of every slice using a point-based navigator correction scheme collected at the beginning of every spiral read-out.…”

Section: Experiments 1: Identification Of Regions Tuned To Reachable Smentioning

confidence: 99%

Is That within Reach? fMRI Reveals That the Human Superior Parieto-Occipital Cortex Encodes Objects Reachable by the Hand

Gallivan¹,

Cavina-Pratesi²,

Culham³

2009

J. Neurosci.

196

173

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Macaque neurophysiology and human neuropsychology results suggest that parietal cortex encodes a unique representation of space within reach of the arm. Here, we used slow event-related functional magnetic resonance imaging (fMRI) to investigate whether human brain areas involved in reaching are more activated by objects within reach versus beyond reach. In experiment 1, graspable objects were placed at three possible locations on a platform: two reachable locations and one beyond reach. On some trials, participants reached to touch or grasp objects at the reachable location; on other trials participants passively viewed objects at one of the three locations. A reach-related area in the superior parieto-occipital cortex (SPOC) was more activated for targets within reach than beyond. In experiment 2, we investigated whether this SPOC response occurred when visual and motor confounds were controlled and whether it was modulated when a tool extended the effective range of the arm. On some trials, participants performed grasping and reaching actions to a reachable object location using either the hand alone or a tool; on other trials, participants passively viewed reachable and unreachable object locations. SPOC was significantly more active for passively viewed objects within reach of the hand versus beyond reach, regardless of whether or not a tool was available. Interestingly, these findings suggest that neural responses within brain areas coding actions (such as SPOC for reaching) may reflect automatic processing of motor affordances (such as reachability with the hand).

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Robust automated shimming technique using arbitrary mapping acquisition parameters (RASTAMAP)

Cited by 84 publications

References 22 publications

Origins of R ₂ ^∗ orientation dependence in gray and white matter

Origins of R ₂ ^∗ orientation dependence in gray and white matter

Functional Networks in the Anesthetized Rat Brain Revealed by Independent Component Analysis of Resting-State fMRI

Is That within Reach? fMRI Reveals That the Human Superior Parieto-Occipital Cortex Encodes Objects Reachable by the Hand

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Robust automated shimming technique using arbitrary mapping acquisition parameters (RASTAMAP)

Cited by 84 publications

References 22 publications

Origins of R 2 ∗ orientation dependence in gray and white matter

Origins of R 2 ∗ orientation dependence in gray and white matter

Functional Networks in the Anesthetized Rat Brain Revealed by Independent Component Analysis of Resting-State fMRI

Is That within Reach? fMRI Reveals That the Human Superior Parieto-Occipital Cortex Encodes Objects Reachable by the Hand

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Origins of R ₂ ^∗ orientation dependence in gray and white matter

Origins of R ₂ ^∗ orientation dependence in gray and white matter