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BOLD response can be fitted using the population receptive field (PRF) model to reveal how visual input is represented on the cortex (Dumoulin and Wandell, 2008). Fitting the PRF model costs considerable time, often requiring days to analyze BOLD signals for a small cohort of subjects. We introduce the qPRF (“quick PRF”), a system for accelerated PRF modeling that reduced the computation time by a factor >1,000 without losing goodness-of-fit when compared to another widely available PRF modeling package (Kay et al., 2013) on a benchmark of data from the Human Connectome Project (HCP; Van Essen et al. (2013). The system achieves this level of acceleration by pre-computing a tree-like data structure, which it rapidly searches during the fitting step for an optimal parameter combination. We tested the method on a constrained four-parameter version of the PRF model (Strategy 1 herein) and an unconstrained five-parameter PRF model, which the qPRF fitted at comparable speed (Strategy 2). We show how an additional search step can guarantee optimality of qPRF solutions with little additional time cost (Strategy 3). To assess the quality of qPRF solutions, we compared our Strategy 1 solutions to those provided by Benson et al. (2018) who performed a similar four-parameter fit. Both hemispheres of the 181 subjects in the HCP dataset (a total of 10,753,572 vertices, each with a unique BOLD time series of 1800 frames) were analyzed by qPRF in 12.82 h on an ordinary CPU. The absolute difference in R2 achieved by the qPRF compared to Benson et al. (2018) was negligible, with a median of 0.025% (R2 units being between 0% and 100%). In general, the qPRF yielded a slightly better fitting solution, achieving a greater R2 on 70.2% of vertices. We also assess the qPRF method’s model-recovery ability using a simulated dataset. The qPRF may facilitate the development and use of more elaborate models based on the PRF framework and may pave the way for novel clinical applications. •We describe a system to perform PRF modeling up to 1,500 times faster than others.•The system achieves equivalent goodness-of-fit as others.•A pre-computed tree and similarity-based search strategy underlie the acceleration.

The three-dimension (3D) magnetization-prepared rapid gradient-echo (MP-RAGE) sequence is one of the most popular sequences for structural brain imaging in clinical and research settings. The sequence captures high tissue contrast and provides high spatial resolution with whole brain coverage in a short scan time. In this paper, we first computed the optimal k-space sampling by optimizing the contrast of simulated images acquired with the MP-RAGE sequence at 3.0 Tesla using computer simulations. Because the software of our scanner has only limited settings for k-space sampling, we then determined the optimal k-space sampling for settings that can be realized on our scanner. Subsequently we optimized several major imaging parameters to maximize normal brain tissue contrasts under the optimal k-space sampling. The optimal parameters are flip angle of 12°, effective inversion time within 900 to 1100 ms, and delay time of 0 ms. In vivo experiments showed that the quality of images acquired with our optimal protocol was significantly higher than that of images obtained using recommended protocols in prior publications. The optimization of k-spacing sampling and imaging parameters significantly improved the quality and detection sensitivity of brain images acquired with MP-RAGE.

The human visual system exhibits non-uniform spatial resolution across the visual field, which is characterized by the cortical magnification factor (CMF) that reflects its anatomical basis. However, current approaches for quantifying CMF using retinotopic maps derived from BOLD functional magnetic resonance imaging (fMRI) are limited by the inherent low signal-to-noise ratio of fMRI data and inaccuracies in the topological relationships of the retinotopic maps. In this study, we introduced a new pipeline to quantify planar CMF from retinotopic maps generated from the population receptive field (pRF) model. The pipeline projected the 3D pRF solutions onto a 2D planar disk, using optimal transport (OT) to preserve local cortical surface areas, and applied topological smoothing to ensure that the resulting retinotopic maps maintain their topology. We then estimated 2D CMF maps from the projected retinotopic maps on the planar disk using the 1-ring patch method. Applying this pipeline to the Human Connectome Project (HCP) 7T dataset, we revealed previously unobserved CMF patterns across the visual field and demonstrated individual differences among the 181 subjects. The pipeline was further validated on the New York University (NYU) 3T dataset, showing reliable and repeatable results. Our study provided new analytical methods and offered novel insights into visual processing. •An integrated framework for quantifying planar cortical magnification factor (CMF).•Optimal transport finds the best area-preserving map between cortex and flat surfaces.•Adaptive smoothing ensures the preservation of topological properties.•The one-ring patch method is used to estimate 2D CMF maps.•Apply planar CMF measurements to explain individual differences in visual perception.

Improvements in performance on visual tasks due to practice are often specific to a retinal position or stimulus feature. Many researchers suggest that specific perceptual learning alters selective retinotopic representations in early visual analysis. However, transfer is almost always practically advantageous, and it does occur. If perceptual learning alters location-specific representations, how does it transfer to new locations? An integrated reweighting theory explains transfer over retinal locations by incorporating higher level location-independent representations into a multilevel learning system. Location transfer is mediated through location-independent representations, whereas stimulus feature transfer is determined by stimulus similarity at both location-specific and location-independent levels. Transfer to new locations/positions differs fundamentally from transfer to new stimuli. After substantial initial training on an orientation discrimination task, switches to a new location or position are compared with switches to new orientations in the same position, or switches of both. Position switches led to the highest degree of transfer, whereas orientation switches led to the highest levels of specificity. A computational model of integrated reweighting is developed and tested that incorporates the details of the stimuli and the experiment. Transfer to an identical orientation task in a new position is mediated via more broadly tuned location-invariant representations, whereas changing orientation in the same position invokes interference or independent learning of the new orientations at both levels, reflecting stimulus dissimilarity. Consistent with single-cell recording studies, perceptual learning alters the weighting of both early and midlevel representations of the visual system.

AimsTo evaluate the association between contrast sensitivity function (CSF) and glaucomatous structural damage in primary open-angle glaucoma (POAG).MethodsA cross-sectional study was performed with 103 patients (103 eyes) aged 25–50 years who had POAG without any other ocular disease. CSF measurements were obtained by the quick CSF method, a novel active learning algorithm that covers 19 spatial frequencies and 128 contrast levels. The peripapillary retinal nerve fibre layer (pRNFL), macular ganglion cell complex (mGCC), radial peripapillary capillary (RPC) and macular vasculature were measured by optical coherence tomography and angiography. Correlation and regression analyses were used to assess the association of area under log CSF (AULCSF), CSF acuity and contrast sensitivities at multiple spatial frequencies with structural parameters.ResultsAULCSF and CSF acuity were positively associated with pRNFL thickness, RPC density, mGCC thickness and superficial macular vessel density (p<0.05). Those parameters were also significantly associated with contrast sensitivity at 1, 1.5, 3, 6, 12, 18 cycles per degree spatial frequencies (p<0.05) and, the lower the spatial frequency, the higher the correlation coefficient. RPC density (p=0.035, p=0.023) and mGCC thickness (p=0.002, p=0.011) had significant predictive value for contrast sensitivity at 1 and 1.5 cycles per degree, with adjusted R 2 of 0.346 and 0.343, respectively.ConclusionsFull spatial frequency contrast sensitivity impairment, most notably at low spatial frequencies, is a characteristic change in POAG. Contrast sensitivity is a potential functional endpoint for the measurement of glaucoma severity.

Retinotopic map, the mapping between visual inputs on the retina and neuronal responses on the cortical surface, is one of the central topics in vision science. Typically, human retinotopic maps are constructed by analyzing functional magnetic resonance responses to designed visual stimuli on the cortical surface. Although it is widely used in visual neuroscience, retinotopic maps are limited by the signal-to-noise ratio and spatial resolution of fMRI. One promising approach to improve the quality of retinotopic maps is to register individual subject’s retinotopic maps to a retinotopic template. However, none of the existing retinotopic registration methods has explicitly quantified the diffeomorphic condition, that is, retinotopic maps shall be aligned by stretching/compressing without tearing up the cortical surface. Here, we developed Diffeomorphic Registration for Retinotopic Maps (DRRM) to simultaneously align retinotopic maps in multiple visual regions under the diffeomorphic condition. Specifically, we used the Beltrami coefficient to model the diffeomorphic condition and performed surface registration based on retinotopic coordinates. The overall framework preserves the topological condition defined in the template. We further developed a unique evaluation protocol and compared the performance of the new method with several existing registration methods on both synthetic and real datasets. The results showed that DRRM is superior to the existing methods in achieving diffeomorphic registration in synthetic and empirical data from 3T and 7T MRI systems. DRRM may improve the interpretation of low-quality retinotopic maps and facilitate applications of retinotopic maps in clinical settings.

We developed and validated digital twins (DTs) for contrast sensitivity function (CSF) across 12 prediction tasks using a data-driven, generative model approach based on a hierarchical Bayesian model (HBM). For each prediction task, we utilized the HBM to compute the joint distribution of CSF hyperparameters and parameters at the population, subject, and test levels. This computation was based on a combination of historical data (N = 56), any new data from additional subjects (N = 56), and “missing data” from unmeasured conditions. The posterior distributions of the parameters in the unmeasured conditions were used as input for the CSF generative model to generate predicted CSFs. In addition to their accuracy and precision, these predictions were evaluated for their potential as informative priors that enable generation of synthetic quantitative contrast sensitivity function (qCSF) data or rescore existing qCSF data. The DTs demonstrated high accuracy in group level predictions across all tasks and maintained accuracy at the individual subject level when new data were available, with accuracy comparable to and precision lower than the observed data. DT predictions could reduce the data collection burden by more than 50% in qCSF testing when using 25 trials. Although further research is necessary, this study demonstrates the potential of DTs in vision assessment. Predictions from DTs could improve the accuracy, precision, and efficiency of vision assessment and enable personalized medicine, offering more efficient and effective patient care solutions.

Significance Recent advances in the field of learning have identified improvement of perceptual templates as a key mechanism underlying training-induced performance enhancements. Here, using a combination of psychophysics and neural modeling, we demonstrate that this mechanism—improved learning of perceptual templates—is also engaged after action video game play. Habitual action gamers or individuals trained to play action games demonstrate perceptual templates better tuned to the task and stimulus at hand than control groups, a difference shown to emerge as learning proceeds. This work further illustrates the importance of the development of improved perceptual templates as a mechanism mediating training and transfer effects and provides a novel account for the surprisingly broad transfer of performance enhancements noted after action game play. The field of perceptual learning has identified changes in perceptual templates as a powerful mechanism mediating the learning of statistical regularities in our environment. By measuring threshold-vs.-contrast curves using an orientation identification task under varying levels of external noise, the perceptual template model (PTM) allows one to disentangle various sources of signal-to-noise changes that can alter performance. We use the PTM approach to elucidate the mechanism that underlies the wide range of improvements noted after action video game play. We show that action video game players make use of improved perceptual templates compared with nonvideo game players, and we confirm a causal role for action video game play in inducing such improvements through a 50-h training study. Then, by adapting a recent neural model to this task, we demonstrate how such improved perceptual templates can arise from reweighting the connectivity between visual areas. Finally, we establish that action gamers do not enter the perceptual task with improved perceptual templates. Instead, although performance in action gamers is initially indistinguishable from that of nongamers, action gamers more rapidly learn the proper template as they experience the task. Taken together, our results establish for the first time to our knowledge the development of enhanced perceptual templates following action game play. Because such an improvement can facilitate the inference of the proper generative model for the task at hand, unlike perceptual learning that is quite specific, it thus elucidates a general learning mechanism that can account for the various behavioral benefits noted after action game play.

Retinotopic mapping, i.e., the mapping between visual inputs on the retina and neuronal activations in cortical visual areas, is one of the central topics in visual neuroscience. For human observers, the mapping is obtained by analyzing functional magnetic resonance imaging (fMRI) signals of cortical responses to slowly moving visual stimuli on the retina. Although it is well known from neurophysiology that the mapping is topological (i.e., the topology of neighborhood connectivity is preserved) within each visual area, retinotopic maps derived from the state-of-the-art methods are often not topological because of the low signal-to-noise ratio and spatial resolution of fMRI. The violation of topological condition is most severe in cortical regions corresponding to the neighborhood of the fovea (e.g., < 1 degree eccentricity in the Human Connectome Project (HCP) dataset), significantly impeding accurate analysis of retinotopic maps. This study aims to directly model the topological condition and generate topology-preserving and smooth retinotopic maps. Specifically, we adopted the Beltrami coefficient, a metric of quasiconformal mapping, to define the topological condition, developed a mathematical model to quantify topological smoothing as a constrained optimization problem, and elaborated an efficient numerical method to solve the problem. The method was then applied to V1, V2, and V3 simultaneously in the HCP dataset. Experiments with both simulated and real retinotopy data demonstrated that the proposed method could generate topological and smooth retinotopic maps.

: Amblyopia and strabismus affect 2%-5% of the population and cause a broad range of visual deficits. The response to treatment is generally assessed using visual acuity, which is an insensitive measure of visual function and may, therefore, underestimate binocular vision gains in these patients. On the other hand, the contrast sensitivity function (CSF) generally takes longer to assess than visual acuity, but it is better correlated with improvement in a range of visual tasks and, notably, with improvements in binocular vision. The present study aims to assess monocular and binocular CSFs in amblyopia and strabismus patients. : Both monocular CSFs and the binocular CSF were assessed for subjects with amblyopia ( = 11), strabismus without amblyopia ( = 20), and normally sighted controls ( = 24) using a tablet-based implementation of the quick CSF, which can assess a full CSF in <3 min. Binocular summation was evaluated against a baseline model of simple probability summation. : The CSF of amblyopic eyes was impaired at mid-to-high spatial frequencies compared to fellow eyes, strabismic eyes without amblyopia, and control eyes. Binocular contrast summation exceeded probability summation in controls, but not in subjects with amblyopia (with or without strabismus) or strabismus without amblyopia who were able to fuse at the test distance. Binocular summation was less than probability summation in strabismic subjects who were unable to fuse. : We conclude that monocular and binocular contrast sensitivity deficits define important characteristics of amblyopia and strabismus that are not captured by visual acuity alone and can be measured efficiently using the quick CSF.