Magnetization transfer weighted EPI facilitates cortical depth determination in native fMRI space.
Ontology highlight
ABSTRACT:
SUBMITTER: Chai Y
PROVIDER: S-EPMC8520138 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:When visual patterns drifting in different directions and/or at different speeds are superimposed on the same plane, observers perceive transparent surfaces on planes of different depths. This phenomenon is known as transparent motion perception. In this study, cortical activities were measured using functional magnetic resonance imaging (fMRI) and magnetoencephalography (MEG) to reveal the cortical dynamics associated with determination of depth order during transparent motion perception. In addition, offline eye movement measurements were performed to determine the latencies of the start of both pursuit eye movements and depth attention that are important in determination of the depth order. MEG and fMRI data were analyzed by a normalized integrative fMRI-MEG method that enables reconstruction of time-varying dipole moments of activated regions from MEG signals. Statistical analysis of fMRI data was performed to identify activated regions. The activated regions were used as spatial constraints for the reconstruction using the integrative fMRI-MEG method. We focused on the period between latencies (216-405 ms) determined by eye movement experiment, which are related to determination of the depth order. The results of integrative analysis revealed that significant neural activities were observed in the visual association area, the human middle temporal area, the intraparietal sulcus, the lateral occipital cortex, and the anterior cingulate cortex between 216 and 405 ms. These results suggest that initial eye movement and accompanying cortical activations during focused duration play an important role in determining the depth order during transparent motion perception.
| S-EPMC6869142 | biostudies-literature
Project description:Spin-echo (SE) BOLD fMRI has high microvascular specificity, and thus provides a more reliable means to localize neural activity compared to conventional gradient-echo BOLD fMRI. However, the most common SE BOLD acquisition method, SE-EPI, is known to suffer from T2' contrast contamination with undesirable draining vein bias. To address this, in this study, we extended a recently developed distortion/blurring-free multi-shot EPI technique, Echo-Planar Time-resolved Imaging (EPTI), to cortical-depth dependent SE-fMRI at 7T to test whether it could provide purer SE BOLD contrast with minimal T2' contamination for improved neuronal specificity. From the same acquisition, the time-resolved feature of EPTI also provides a series of asymmetric SE (ASE) images with varying T2' weightings, and enables extraction of data equivalent to conventional SE EPI with different echo train lengths (ETLs). This allows us to systematically examine how T2'-contribution affects different SE acquisition strategies using a single dataset. A low-rank spatiotemporal subspace reconstruction was implemented for the SE-EPTI acquisition, which incorporates corrections for both shot-to-shot phase variations and dynamic B0 drifts. SE-EPTI was used in a visual task fMRI experiment to demonstrate that i) the pure SE image provided by EPTI results in the highest microvascular specificity; ii) the ASE EPTI series, with a graded introduction of T2' weightings at time points farther away from the pure SE, show a gradual sensitivity increase along with increasing draining vein bias; iii) the longer ETL seen in conventional SE EPI acquisitions will induce more draining vein bias. Consistent results were observed across multiple subjects, demonstrating the robustness of the proposed technique for SE-BOLD fMRI with high specificity.
| S-EPMC8820652 | biostudies-literature
Project description:Neural activity in early visual cortex is modulated by luminance contrast. Cortical depth (i.e., laminar) contrast responses have been studied in monkey early visual cortex, but not in humans. In addition to the high spatial resolution needed and the ensuing low signal-to-noise ratio, laminar studies in humans using fMRI are hampered by the strong venous vascular weighting of the fMRI signal. In this study, we measured luminance contrast responses in human V1 and V2 with high-resolution fMRI at 7 T. To account for the effect of intracortical ascending veins, we applied a novel spatial deconvolution model to the fMRI depth profiles. Before spatial deconvolution, the contrast response in V1 showed a slight local maximum at mid cortical depth, whereas V2 exhibited a monotonic signal increase toward the cortical surface. After applying the deconvolution, both V1 and V2 showed a pronounced local maximum at mid cortical depth, with an additional peak in deep grey matter, especially in V1. Moreover, we found a difference in contrast sensitivity between V1 and V2, but no evidence for variations in contrast sensitivity as a function of cortical depth. These findings are in agreement with results obtained in nonhuman primates, but further research will be needed to validate the spatial deconvolution approach.
| S-EPMC6866457 | biostudies-literature
Project description:BackgroundDetecting cortical demyelination using magnetic resonance imaging (MRI) in multiple sclerosis (MS) remains a challenge. Magnetization transfer ratio (MTR), T1-weighted/T2-weighted ratio (T1T2R), and T2-weighted (T2w) signal are sensitive to cortical demyelination, but their accuracy is unknown.ObjectivesTo quantify the sensitivity, specificity, and accuracy of postmortem T1T2R, MTR, and T2w in detecting cortical demyelination.MethodsIn situ postmortem MRIs from 9 patients were used to measure T1T2R, MTR, and T2w along the midline of cortical gray matter and classified as normal or abnormal. MRIs were co-registered and compared to hemispheric myelin staining. The sensitivity, specificity, and accuracy of T1T2R, MTR, and T2w in detecting cortical demyelination were measured.ResultsThe mean age (standard deviation) at death was 64.7 (+/-13.7) years with a disease duration of 23.8 (+/-10.5) years. The sensitivity was 78% for MTR, 75% for T1T2R, and 63% for T2w. The specificity was 46% (T2w), 13% (T1T2R), and 29% (MTR). The accuracy was 71% (T2w), 39% (MTR), and 42% (T1T2R). There were no significant differences between different MRI measures in cortical demyelination or intracortical/subpial lesion detection.ConclusionsAlthough somewhat sensitive, the modest specificity of conventional MRI modalities for cortical demyelination indicates that they are influenced by cortical changes other than demyelination. Improved acquisition and post-processing are needed to reliably measure cortical lesion load.
| S-EPMC8605037 | biostudies-literature
Project description:Compressed sensing (CS) may be useful for accelerating data acquisitions in high-resolution fMRI. However, due to the inherent slow temporal dynamics of the hemodynamic signals and concerns of potential statistical power loss, the CS approach for fMRI (CS-fMRI) has not been extensively investigated. To evaluate the utility of CS in fMRI application, we systematically investigated the properties of CS-fMRI using computer simulations and in vivo experiments of rat forepaw sensory and odor stimulations with gradient-recalled echo (GRE) and echo planar imaging (EPI) sequences. Various undersampling patterns along the phase-encoding direction were studied and k-t FOCUSS was used as the CS reconstruction algorithm, which exploits the temporal redundancy of images. Functional sensitivity, specificity, and time courses were compared between fully-sampled and CS-fMRI with reduction factors of 2 and 4. CS-fMRI with GRE, but not with EPI, improves the statistical sensitivity for activation detection over the fully sampled data when the ratio of the fMRI signal change to noise is low. CS improves the temporal resolution and reduces temporal noise correlations. While CS reduces the functional response amplitudes, the noise variance is also reduced to make the overall activation detection more sensitive. Consequently, CS is a valuable fMRI acceleration approach, especially for GRE fMRI studies.
| S-EPMC4021580 | biostudies-literature
Project description:ObjectivesTo assess the sensitivity of stimulated echo acquisition mode diffusion weighted imaging (STEAM-DWI) to ischemic stroke in comparison to echo-planar imaging diffusion weighted imaging (EPI-DWI) in the infratentorial compartment.MethodsFifty-seven patients presenting with clinical features of infratentorial stroke underwent STEAM-DWI, high-resolution EPI-DWI (HR-DWI, 2.5 mm slice thickness) and low-resolution EPI-DWI (LR-DWI, 5 mm slice thickness). Four readers assessed the presence of ischemic lesions and artifacts. Agreement between sequences and interobserver agreement on the presence of ischemia were calculated. The sensitivities of the DWI sequences were calculated in 45 patients with a confirmed diagnosis of infratentorial stroke.ResultsMedian time from symptom onset to imaging was 24 hours. STEAM-DWI agreed with LR-DWI in 89.5% of cases (kappa = 0.72, p<0.0001) and with HR-DWI in 89.5% of cases (kappa = 0.68, p<0.0001). STEAM-DWI showed fewer intraparenchymal artifacts (1/57) than HR-DWI (44/57) and LR-DWI (41/57). Ischemia was visible in 87% of cases for LR-DWI, 93% of cases for HR-DWI, and 89% of cases for STEAM-DWI. Interobserver agreement was good for STEAM-DWI (kappa = 0.62, p<0.0001).ConclusionsCompared to the best currently available MR sequence for detecting ischemia (HR-DWI), STEAM-DWI shows fewer artifacts and a similar sensitivity to infratentorial stroke.
| S-EPMC4987060 | biostudies-literature
Project description:Flying insects, such as flies or bees, rely on consistent information regarding the depth structure of the environment when performing their flight maneuvers in cluttered natural environments. These behaviors include avoiding collisions, approaching targets or spatial navigation. Insects are thought to obtain depth information visually from the retinal image displacements ("optic flow") during translational ego-motion. Optic flow in the insect visual system is processed by a mechanism that can be modeled by correlation-type elementary motion detectors (EMDs). However, it is still an open question how spatial information can be extracted reliably from the responses of the highly contrast- and pattern-dependent EMD responses, especially if the vast range of light intensities encountered in natural environments is taken into account. This question will be addressed here by systematically modeling the peripheral visual system of flies, including various adaptive mechanisms. Different model variants of the peripheral visual system were stimulated with image sequences that mimic the panoramic visual input during translational ego-motion in various natural environments, and the resulting peripheral signals were fed into an array of EMDs. We characterized the influence of each peripheral computational unit on the representation of spatial information in the EMD responses. Our model simulations reveal that information about the overall light level needs to be eliminated from the EMD input as is accomplished under light-adapted conditions in the insect peripheral visual system. The response characteristics of large monopolar cells (LMCs) resemble that of a band-pass filter, which reduces the contrast dependency of EMDs strongly, effectively enhancing the representation of the nearness of objects and, especially, of their contours. We furthermore show that local brightness adaptation of photoreceptors allows for spatial vision under a wide range of dynamic light conditions.
| S-EPMC5073142 | biostudies-literature
Project description:To investigate the saturation-power dependence of amide proton transfer (APT)-weighted and nuclear Overhauser enhancement-weighted image contrasts in a rat glioma model at 4.7 T.The 9L tumor-bearing rats (n = 8) and fresh chicken eggs (n = 4) were scanned on a 4.7-T animal magnetic resonance imaging scanner. Z-spectra over an offset range of ±6 ppm were acquired with different saturation powers, followed by the magnetization transfer-ratio asymmetry analyses around the water resonance.The nuclear Overhauser enhancement signal upfield from the water resonance (-2.5 to -5 ppm) was clearly visible at lower saturation powers (e.g., 0.6 µT) and was larger in the contralateral normal brain tissue than in the tumor. Conversely, the APT effect downfield from the water resonance was maximized at relatively higher saturation powers (e.g., 2.1 µT) and was larger in the tumor than in the contralateral normal brain tissue. The nuclear Overhauser enhancement decreased the APT-weighted image signal, based on the magnetization transfer-ratio asymmetry analysis, but increased the APT-weighted image contrast between the tumor and contralateral normal brain tissue.The APT and nuclear Overhauser enhancement image signals in tumor are maximized at different saturation powers. The saturation power of roughly 2 ?T is ideal for APT-weighted imaging at clinical B0 field strengths.
| S-EPMC3723702 | biostudies-literature
Project description:Resting-state functional magnetic resonance imaging (fMRI) has drastically expanded the scope of brain research by advancing our knowledge about the topologies, dynamics, and interspecies translatability of functional brain networks. Several databases have been developed and shared in accordance with recent key initiatives in the rodent fMRI community to enhance the transparency, reproducibility, and interpretability of data acquired at various sites. Despite these pioneering efforts, one notable challenge preventing efficient standardization in the field is the customary choice of anisotropic echo planar imaging (EPI) schemes with limited spatial coverage. Imaging with anisotropic resolution and/or reduced brain coverage has significant shortcomings including reduced registration accuracy and increased deviation in brain feature detection. Here we proposed a high-spatial-resolution (0.4 mm), isotropic, whole-brain EPI protocol for the rat brain using a horizontal slicing scheme that can maintain a functionally relevant repetition time (TR), avoid high gradient duty cycles, and offer unequivocal whole-brain coverage. Using this protocol, we acquired resting-state EPI fMRI data from 87 healthy rats under the widely used dexmedetomidine sedation supplemented with low-dose isoflurane on a 9.4 T MRI system. We developed an EPI template that closely approximates the Paxinos and Watson's rat brain coordinate system and demonstrated its ability to improve the accuracy of group-level approaches and streamline fMRI data pre-processing. Using this database, we employed a multi-scale dictionary-learning approach to identify reliable spatiotemporal features representing rat brain intrinsic activity. Subsequently, we performed k-means clustering on those features to obtain spatially discrete, functional regions of interest (ROIs). Using Euclidean-based hierarchical clustering and modularity-based partitioning, we identified the topological organizations of the rat brain. Additionally, the identified group-level FC network appeared robust across strains and sexes. The "triple-network" commonly adapted in human fMRI were resembled in the rat brain. Through this work, we disseminate raw and pre-processed isotropic EPI data, a rat brain EPI template, as well as identified functional ROIs and networks in standardized rat brain coordinates. We also make our analytical pipelines and scripts publicly available, with the hope of facilitating rat brain resting-state fMRI study standardization.
| S-EPMC8561231 | biostudies-literature
Project description:The pattern of interregional functional MRI correlations at rest is being actively considered as a potential noninvasive biomarker in multiple diseases. Before such methods can be used in clinical studies it is important to establish their usefulness in three ways. First, the long-term stability of resting correlation patterns should be characterized, but there have been very few such studies. Second, analysis of resting correlations should account for the unique neuroanatomy of each subject by taking measurements in native space and avoiding transformation of functional data to a standard volume space (e.g., Talairach-Tournox or Montreal Neurological Institute atlases). Transformation to a standard volume space has been shown to variably influence the measurement of functional correlations, and this is a particular concern in diseases which may cause structural changes in the brain. Third, comparisons within the patient population of interest and comparisons between patients and age-matched controls, should demonstrate sensitivity to any disease-related disruption of resting functional correlations. Here we examine the test-retest stability of resting fMRI correlations over a period of one year in a group of healthy adults and in a group of cognitively intact individuals who are gene-positive for Huntington's disease. A recently-developed method is used to measure functional correlations in the native space of individual subjects. The utility of resting functional correlations as a biomarker in premanifest Huntington's disease is also investigated. Results in control and premanifest Huntington's populations were both highly consistent at the group level over one year. We thus show that when resting fMRI analysis is performed in native space (to reduce confounds in registration between subjects and groups) it has good long-term stability at the group level. Individual-subject level results were less consistent between visit 1 and visit 2, suggesting further work is required before resting fMRI correlations can be useful diagnostically for individual patients. No significant effect of premanifest Huntington's disease on prespecified interregional fMRI correlations was observed relative to the control group using either baseline or longitudinal measures. Within the premanifest Huntington's group, though, there was evidence that decreased striatal functional correlations might be associated with disease severity, as gauged by estimated years to symptom onset or by striatal volume.
| S-EPMC3254727 | biostudies-literature