Fiber orientation-dependent white matter contrast in gradient echo MRI.
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ABSTRACT:
SUBMITTER: Wharton S
PROVIDER: S-EPMC3494918 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:To investigate B0 -field-orientation dependent white matter contrast in the human brainstem based on R2 * and frequency difference (?f) mapping from gradient echo (GRE) imaging at 11.7T.Multi-echo GRE data were acquired from two fixed human brainstem specimens at multiple orientations with respect to the static B0 field. The B0 -orientation dependent modulation curves of R2 * and ?f measurements between short and long echo time regimes were used to reconstruct maps of three-dimensional (3D) white matter orientation vectors. The results were compared with maps from diffusion MRI, susceptibility tensor imaging, and histological staining of the same specimens.R2 * and ?f maps demonstrated distinct and significant contrast modulation between the corticospinal tract (CST) and transverse pontine fibers (TPF) dependent on B0 orientation. Interleaved fiber orientations of the CST and TPF could be sensitively resolved based on field-orientation-dependent fitting of the R2 * and ?f measurements. The fitted 3D orientation vector maps and peak-to-peak amplitude of R2 * and ?f modulation exhibited close correspondence to primary eigenvector and anisotropy maps derived from diffusion MRI. The amplitude of B0 -orientation dependent R2 * modulation was significantly (P < 0.005) higher in the CST compared with TPF, while fractional anisotropies were comparable.The findings of this study demonstrate the potential of B0 -orientation dependent susceptibility-induced R2 * and ?f contrasts to probe tract-specific orientation and microstructure in white matter. Magn Reson Med 75:2455-2463, 2016. © 2016 Wiley Periodicals, Inc.
| S-EPMC4865411 | biostudies-literature
Project description:To optimize the white-matter-nulled (WMn) Magnetization Prepared Rapid Gradient Echo (MP-RAGE) sequence at 7 Tesla (T), with comparisons to 3T.Optimal parameters for maximizing signal-to-noise ratio (SNR) efficiency were derived. The effect of flip angle and repetition time (TR) on image blurring was modeled using simulations and validated in vivo. A novel two-dimensional (2D) -centric radial fan beam (RFB) k-space segmentation scheme was used to shorten scan times and improve parallel imaging. Healthy subjects as well as patients with multiple sclerosis and tremor were scanned using the optimized protocols.Inversion repetition times (TS) of 4.5 s and 6 s were found to yield the highest SNR efficiency for WMn MP-RAGE at 3T and 7T, respectively. Blurring was more sensitive to flip in WMn than in CSFn MP-RAGE and relatively insensitive to TR for both regimes. The 2D RFB scheme had 19% and 47% higher thalamic SNR and SNR efficiency than the 1D centric scheme for WMn MP-RAGE. Compared with 3T, SNR and SNR efficiency were higher for the 7T WMn regime by 56% and 41%, respectively. MS lesions in the cortex and thalamus as well as thalamic subnuclei in tremor patients were clearly delineated using WMn MP-RAGE.Optimization and new view ordering enabled MP-RAGE imaging with 0.8-1 mm(3) isotropic spatial resolution in scan times of 5 min with whole brain coverage.
| S-EPMC4247820 | biostudies-literature
Project description:Background Myocardial oxygenation imaging could help determine the presence of microvascular dysfunction associated with increased cardiovascular risk. However, it is challenging to depict the potentially small oxygenation alterations with current noninvasive cardiac MRI blood oxygen level-dependent (BOLD) techniques. Purpose To demonstrate the cardiac application of a gradient-echo spin-echo (GESE) echo-planar imaging sequence for dynamic and quantitative heartbeat-to-heartbeat BOLD MRI and evaluate the sequence in populations both healthy and with hypertension in combination with a breath hold-induced CO2 intervention. Materials and Methods GESE echo-planar imaging sequence was performed in 18 healthy participants and in eight prospectively recruited participants with hypertension on a 3.0-T MRI system. T2 and T2* maps were calculated per heartbeat with a four-parameter fitting technique. Septal regions of interests were used to determine T2 and T2* values per heartbeat and examined over the course of a breath hold to determine BOLD changes. T2 and T2* changes of healthy participants and participants with hypertension were compared by using a nonparametric Mann-Whitney test. Results GESE echo-planar imaging approach gave spatially stable T2 and T2* maps per heartbeat for healthy participants and participants with hypertension, with mean T2 values of 43 msec ± 5 (standard deviation) and 46 msec ± 9, respectively, and mean T2* values of 28 msec ± 5 and 22 msec ± 5, respectively. The healthy participants exhibited increasing T2 and T2* values over the course of a breath hold with a mean positive slope of 0.2 msec per heartbeat ± 0.1 for T2 and 0.2 msec per heartbeat ± 0.1 for T2*, whereas for participants with hypertension these dynamic T2 and T2* values had a mean negative slope of -0.2 msec per heartbeat ± 0.2 for T2 and -0.1 msec per heartbeat ± 0.2 for T2*. The difference in these mean slopes between healthy participants and participants with hypertension was significant for both T2 (P < .001) and T2* (P < .001). Conclusion Gradient-echo spin-echo echo-planar imaging sequence provided quantitative T2 and T2* maps per heartbeat and enabled dynamic heartbeat-to-heartbeat blood oxygen level-dependent (BOLD)-response imaging by analyzing changes in T2 and T2* over the time of a breath-hold intervention. This approach could identify differences in the BOLD response between healthy participants and participants with hypertension. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Friedrich in this issue.
| S-EPMC7053244 | biostudies-literature
Project description:Axon diameter mapping using high-gradient diffusion MRI has generated great interest as a noninvasive tool for studying trends in axonal size in the human brain. One of the main barriers to mapping axon diameter across the whole brain is accounting for complex white matter fiber configurations (e.g., crossings and fanning), which are prevalent throughout the brain. Here, we present a framework for generalizing axon diameter index estimation to the whole brain independent of the underlying fiber orientation distribution using the spherical mean technique (SMT). This approach is shown to significantly benefit from the use of real-valued diffusion data with Gaussian noise, which reduces the systematic bias in the estimated parameters resulting from the elevation of the noise floor when using magnitude data with Rician noise. We demonstrate the feasibility of obtaining whole-brain orientationally invariant estimates of axon diameter index and relative volume fractions in six healthy human volunteers using real-valued diffusion data acquired on a dedicated high-gradient 3-Tesla human MRI scanner with 300 mT/m maximum gradient strength. The trends in axon diameter index are consistent with known variations in axon diameter from histology and demonstrate the potential of this generalized framework for revealing coherent patterns in axonal structure throughout the living human brain. The use of real-valued diffusion data provides a viable solution for eliminating the Rician noise floor and should be considered for all spherical mean approaches to microstructural parameter estimation.
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Project description:Diffusion MRI (dMRI) represents one of the few methods for mapping brain fiber orientations non-invasively. Unfortunately, dMRI fiber mapping is an indirect method that relies on inference from measured diffusion patterns. Comparing dMRI results with other modalities is a way to improve the interpretation of dMRI data and help advance dMRI technologies. Here, we present methods for comparing dMRI fiber orientation estimates with optical imaging of fluorescently labeled neurofilaments and vasculature in 3D human and primate brain tissue cuboids cleared using CLARITY. The recent advancements in tissue clearing provide a new opportunity to histologically map fibers projecting in 3D, which represents a captivating complement to dMRI measurements. In this work, we demonstrate the capability to directly compare dMRI and CLARITY in the same human brain tissue and assess multiple approaches for extracting fiber orientation estimates from CLARITY data. We estimate the three-dimensional neuronal fiber and vasculature orientations from neurofilament and vasculature stained CLARITY images by calculating the tertiary eigenvector of structure tensors. We then extend CLARITY orientation estimates to an orientation distribution function (ODF) formalism by summing multiple sub-voxel structure tensor orientation estimates. In a sample containing part of the human thalamus, there is a mean angular difference of 19o±15o between the primary eigenvectors of the dMRI tensors and the tertiary eigenvectors from the CLARITY neurofilament stain. We also demonstrate evidence that vascular compartments do not affect the dMRI orientation estimates by showing an apparent lack of correspondence (mean angular difference = 49o±23o) between the orientation of the dMRI tensors and the structure tensors in the vasculature stained CLARITY images. In a macaque brain dataset, we examine how the CLARITY feature extraction depends on the chosen feature extraction parameters. By varying the volume of tissue over which the structure tensor estimates are derived, we show that orientation estimates are noisier with more spurious ODF peaks for sub-voxels below 30 µm3 and that, for our data, the optimal gray matter sub-voxel size is between 62.5 µm3 and 125 µm3. The example experiments presented here represent an important advancement towards robust multi-modal MRI-CLARITY comparisons.
| S-EPMC7953593 | biostudies-literature
Project description:Larmor-frequency shift or image phase measured by gradient-echo sequences has provided a new source of MRI contrast. This contrast is being used to study both the structure and function of the brain. So far, phase images of the brain have been largely obtained at long echo times as maximum phase signal-to-noise ratio (SNR) is achieved at TE = T2* (∼40 ms at 3T). The structures of the brain, however, are compartmentalized and complex with a wide range of signal relaxation times. At such long TE, the short-T2 components are largely attenuated and contribute minimally to phase contrast. The purpose of this study was to determine whether proton gradient-echo images of the brain exhibit phase contrast at ultra-short TE (UTE). Our data showed that UTE images acquired at 7 T without off-resonance saturation do not contain significant phase contrast between gray and white matter. However, UTE images of the brain can attain strong phase contrast even at a nominal TE of 106 μs by using off-resonance RF saturation pulses, which provide direct saturation of ultra-short-T2 components and indirect saturation of longer-T2 components via magnetization transfer. In addition, phase contrast between gray and white matter acquired at UTE with off-resonance saturation is reversed compared to that of the long-T2 signals acquired at long TEs. This finding opens up a potential new way to manipulate image phase contrast of the brain. By accessing short and ultra-short-T2 species, MRI phase images may further improve the characterization of tissue microstructure in the brain.
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Project description:PurposeThe multi-exponential T2 decay of the MRI signal from cerebral white matter can be separated into short T2 components related to myelin water and long T2 components related to intracellular and extracellular water. In this study, we investigated to what degree the apparent myelin water fraction (MWF) depends on the angle between white matter fibers and the main magnetic field.MethodsMaps of the apparent MWF were acquired using multi-echo Carr-Purcell-Meiboom-Gill and gradient-echo spin-echo sequences. The Carr-Purcell-Meiboom-Gill sequence was acquired with a TR of 1073 ms, 1500 ms, and 2000 ms. The fiber orientation was mapped with DTI. By angle-wise pooling the voxels across the brain's white matter, orientation-dependent apparent MWF curves were generated.ResultsWe found that the apparent MWF varied between 25% and 35% across different fiber orientations. Furthermore, the selection of the TR influences the apparent MWF.ConclusionWhite matter fiber orientation induces a strong systematic bias on the estimation of the apparent MWF. This finding has implications for future research and the interpretation of MWI results in previously published studies.
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Project description:BackgroundMultiple sclerosis (MS) is a chronic disease affecting the human central nervous system (CNS) and leading to neurologic disability. Although conventional MRI techniques can readily detect focal white matter (WM) lesions, it remains challenging to quantify tissue damage in normal-appearing gray matter (GM) and WM.PurposeTo demonstrate that a new MRI biomarker, R2t*, can provide quantitative analysis of tissue damage across the brain in MS patients in a single scan.Study typeProspective.SubjectsForty-four MS patients and 19 healthy controls (HC).Field strength/sequence3T, quantitative gradient-recalled-echo (qGRE), Magnetization-prepared rapid gradient-echo, fluid-attenuated inversion recovery.AssessmentSeverity of tissue damage was assessed by reduced R2t*. Tissue atrophy was assessed by cortical thickness and cervical spinal cord cross-sectional area (CSA). Multiple Sclerosis Functional Composite was used for clinical assessment.ResultsR2t* in cortical GM was more sensitive to MS damage than cortical atrophy. Using more than two standard deviations (SD) reduction versus age-matched HC as the cutoff, 48% of MS patients showed lower R2t*, versus only 9% with lower cortical thickness. Significant correlations between severities of tissue injury were identified among 1) upper cervical cord and several cortical regions, including motor cortex (P < 0.001), and 2) adjacent regions of GM and subcortical WM (P < 0.001). R2t*-defined tissue cellular damage in cortical GM was greater relative to adjacent WM. Reductions in cortical R2t* correlated with cognitive impairment (P < 0.01). Motor-related clinical signs correlated most with cervical cord CSA (P < 0.001).Data conclusionReductions in R2t* within cortical GM was more sensitive to tissue damage than atrophy, potentially allowing a reduced sample size in clinical trials. R2t* together with structural morphometry suggested topographic patterns of regions showing correlated tissue damage throughout the brain and the cervical spinal cord of MS patients.Level of evidence2 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2019;49:487-498.
| S-EPMC6423972 | biostudies-literature
Project description:Diffusion tensor imaging (DTI) studies of human brain development have consistently shown widespread, but nonlinear increases in white matter anisotropy through childhood, adolescence, and into adulthood. However, despite its sensitivity to changes in tissue microstructure, DTI lacks the specificity to disentangle distinct microstructural features of white and gray matter. Neurite orientation dispersion and density imaging (NODDI) is a recently proposed multi-compartment biophysical model of brain microstructure that can estimate non-collinear properties of white matter, such as neurite orientation dispersion index (ODI) and neurite density index (NDI). In this study, we apply NODDI to 66 healthy controls aged 7-63 years to investigate changes of ODI and NDI with brain maturation, with comparison to standard DTI metrics. Using both region-of-interest and voxel-wise analyses, we find that NDI exhibits striking increases over the studied age range following a logarithmic growth pattern, while ODI rises following an exponential growth pattern. This novel finding is consistent with well-established age-related changes of FA over the lifespan that show growth during childhood and adolescence, plateau during early adulthood, and accelerating decay after the fourth decade of life. Our results suggest that the rise of FA during the first two decades of life is dominated by increasing NDI, while the fall in FA after the fourth decade is driven by the exponential rise of ODI that overcomes the slower increases of NDI. Using partial least squares regression, we further demonstrate that NODDI better predicts chronological age than DTI. Finally, we show excellent test-retest reliability of NODDI metrics, with coefficients of variation below 5% in all measured regions of interest. Our results support the conclusion that NODDI reveals biologically specific characteristics of brain development that are more closely linked to the microstructural features of white matter than are the empirical metrics provided by DTI.
| S-EPMC4482659 | biostudies-literature
Project description:PurposeSensitivity and specificity of blood oxygenation level-dependent (BOLD) functional MRI (fMRI) is sensitive to magnetic field strength and acquisition methods. We have investigated gradient-echo (GE)- and spin-echo (SE)-BOLD fMRI at ultrahigh fields of 9.4 and 15.2 Tesla.MethodsBOLD fMRI experiments responding to forepaw stimulation were performed with 3 echo times (TE) at each echo type and B0 in α-chloralose-anesthetized rats. The contralateral forelimb somatosensory region was selected for quantitative analyses.ResultsAt 9.4 T and 15.2 T, average baseline T2 * (n = 9) was 26.6 and 17.1 msec, whereas baseline T2 value (n = 9) was 35.7 and 24.5 msec, respectively. Averaged stimulation-induced ΔR2 * was -1.72 s-1 at 9.4 T and -3.09 s-1 at 15.2 T, whereas ΔR2 was -1.19 s-1 at 9.4 T and -1.97 s-1 at 15.2 T. At the optimal TE of tissue T2 * or T2 , BOLD percent changes were slightly higher at 15.2 T than at 9.4 T (GE: 7.4% versus 6.4% and SE: 5.7% versus 5.4%). The ΔR2 * and ΔR2 ratio of 15.2 T to 9.4 T was 1.8 and 1.66, respectively. The ratio of the macrovessel-containing superficial to microvessel-dominant parenchymal BOLD signal was 1.73 to 1.76 for GE-BOLD versus 1.13 to 1.19 for SE-BOLD, indicating that the SE-BOLD contrast is less sensitive to macrovessels than GE-BOLD.ConclusionSE-BOLD fMRI improves spatial specificity to microvessels compared to GE-BOLD at both fields. BOLD sensitivity is similar at the both fields and can be improved at ultrahigh fields only for thermal-noise-dominant ultrahigh-resolution fMRI.
| S-EPMC6585650 | biostudies-literature