Biology subjects

Kurzawski, J. W.

Publications and source records attributed to Kurzawski, J. W..

12 recordsLinked to original sources

bioRxiv2026

A critical assessment of LGN segmentation quality based on volume, contour, and location

Reliable segmentation of the lateral geniculate nucleus (LGN), a small thalamic relay nucleus essential for visual processing, is necessary for characterizing its anatomy in healthy populations and structural alterations in neurological disorders. However, accurate delineation remains challenging on routinely acquired T1-weighted images because the LGN is small, deeply located, and has limited contrast relative to surrounding thalamic tissue. Although manual segmentation remains the reference standard, it is time consuming and susceptible to rater variability, limiting its use in large datasets. Automated approaches may therefore provide a more scalable alternative. In this study, we performed a systematic benchmarking of seven automated approaches: FreeSurfer, NextBrain, DeepThalamus, HIPS-THOMAS, MASSP 2.0, BigBrain alignment, and manual novice segmentation against expert-defined ground truth. We applied a multi-metric evaluation incorporating the Dice similarity coefficient, Hausdorff distance and balanced average Hausdorff distance, volumetric similarity, and Euclidean distance. Together, these measures evaluate overlap, contour, volume, and location against expert manual segmentations. Our results indicate that HIPS-THOMAS and DeepThalamus outperformed the other automated methods in all metrics. However, manual segmentation retained high precision despite exhibiting greater inter-subject variance than the top-performing automated segmentation tools. The different metrics do not necessarily report the same order of quality, highlighting the need of using multiple metrics for evaluation segmentation quality.

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bioRxiv2026

Object recognition along the ventral stream: effects of visual noise

How does the visual system recognize objects in natural environments? Here, we investigate the neural computations underlying robust object recognition along the ventral stream. We adapted psychophysical critical-band masking to fMRI, measuring BOLD responses along the ventral stream to natural images perturbed by bandpass noise. We found that, along this stream, the overall BOLD response to noise alone is sensitive to an increasingly wide range of stimulus spatial frequency, from 2 octaves in V1 to 5 octaves in ventral temporal cortex (VTC). However, when we assess the effect of the same noise on the accuracy of decoding scene images from the BOLD response, we obtain a different result: Recognition bandwidth is conserved along the ventral stream at about 2 octaves, close to the 1.5-octave behavioral channel. Though the recognition band is conserved, its noise tolerance increases steadily along the ventral stream, approaching behavioral levels in VTC. These findings suggest that V1 sets the bandwidth of the object-recognition channel, while downstream areas progressively denoise the signal, establishing the channels noise tolerance. This biological architecture--early channel isolation followed by successive denoising--may explain why human vision remains more robust than current machine vision.

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bioRxiv2025

The pulvinar regulates plasticity in human visual cortex

In normally sighted human adults, two-hours of monocular deprivation is sufficient to transiently alter ocular dominance. Here we show that this is associated with a reduction of functional connectivity between the pulvinar and early visual cortex, selective for the pulvinar-to-V1 directionality. Across participants, the strength of the pulvinar-to-V1 connectivity was negatively correlated with the ocular dominance shift, implying less plasticity in participants with stronger influence of the pulvinar over V1. Our results support a revised model of adult V1 plasticity, where short-term reorganization is gated by modulatory signals relayed by the pulvinar. TeaserShort-term monocular deprivation triggers a reorganization of the visual processing network, measured with 7TfMRI in human adults.

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bioRxiv2024

Conservation of cortical crowding distance across individuals in human V4

Visual recognition is limited by both object size (acuity) and spacing. The spacing limit, called "crowding", is the failure to recognize an object in the presence of other objects. Here, we take advantage of individual differences in crowding to investigate its biological basis. Crowding distance, the minimum object spacing needed for recognition, varies 2-fold among healthy adults. We test the conjecture that this variation in psychophysical crowding distance is due to variation in cortical map size. To test this, we made paired measurements of brain and behavior in 50 observers. We used psychophysics to measure crowding distance and calculate{lambda} , the number of letters that fit into each observers visual field without crowding. In the same observers, we used fMRI to measure the surface area A (mm{superscript 2}) of retinotopic maps V1, V2, V3, and V4. Across observers,{lambda} is proportional to the surface area of V4 but is uncorrelated with the surface area of V1 to V3. The proportional relationship of{lambda} to area of V4 indicates conservation of cortical crowding distance across individuals: letters can be recognized if they are spaced by at least 1.4 mm on the V4 map, irrespective of map size and psychophysical crowding distance. We conclude that the size of V4 predicts the spacing limit of visual perception.

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bioRxiv2023

EasyEyes - Accurate fixation for online vision testing of crowding and beyond

Online methods allow testing of larger, more diverse populations, with much less effort than in-lab testing. However, many psychophysical measurements, including visual crowding, require accurate eye fixation, which is classically achieved by testing only experienced observers who have learned to fixate reliably, or by using a gaze tracker to restrict testing to moments when fixation is accurate. Alas, both approaches are impractical online since online observers tend to be inexperienced, and online gaze tracking, using the built-in webcam, has a low precision ({+/-}4 deg, Papoutsaki et al., 2016). The EasyEyes open-source software reliably measures peripheral thresholds online with accurate fixation achieved in a novel way, without gaze tracking. EasyEyes tells observers to use the cursor to track a moving crosshair. At a random time during successful tracking, a brief target is presented in the periphery. The observer responds by identifying the target. To evaluate EasyEyes fixation accuracy and thresholds, we tested 12 naive observers in three ways in a counterbalanced order: first, in the lab, using gaze-contingent stimulus presentation (Kurzawski et al., 2023; Pelli et al., 2016); second, in the lab, using EasyEyes while independently monitoring gaze; third, online at home, using EasyEyes. We find that crowding thresholds are consistent (no significant differences in mean and variance of thresholds across ways) and individual differences are conserved. The small root mean square (RMS) fixation error (0.6 deg) during target presentation eliminates the need for gaze tracking. Thus, EasyEyes enables fixation-dependent measurements online, for easy testing of larger and more diverse populations.

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bioRxiv2022

GLMsingle: a toolbox for improving single-trial fMRI response estimates

Advances in modern artificial intelligence (AI) have inspired a paradigm shift in human neuroscience, yielding large-scale functional magnetic resonance imaging (fMRI) datasets that provide high-resolution brain responses to tens of thousands of naturalistic visual stimuli. Because such experiments necessarily involve brief stimulus durations and few repetitions of each stimulus, achieving sufficient signal-to-noise ratio can be a major challenge. We address this challenge by introducing GLMsingle, a scalable, user-friendly toolbox available in MATLAB and Python that enables accurate estimation of single-trial fMRI responses (glmsingle.org). Requiring only fMRI time-series data and a design matrix as inputs, GLMsingle integrates three techniques for improving the accuracy of trial-wise general linear model (GLM) beta estimates. First, for each voxel, a custom hemodynamic response function (HRF) is identified from a library of candidate functions. Second, cross-validation is used to derive a set of noise regressors from voxels unrelated to the experimental paradigm. Third, to improve the stability of beta estimates for closely spaced trials, betas are regularized on a voxel-wise basis using ridge regression. Applying GLMsingle to the Natural Scenes Dataset and BOLD5000, we find that GLMsingle substantially improves the reliability of beta estimates across visually-responsive cortex in all subjects. Furthermore, these improvements translate into tangible benefits for higher-level analyses relevant to systems and cognitive neuroscience. Specifically, we demonstrate that GLMsingle: (i) improves the decorrelation of response estimates between trials that are nearby in time; (ii) enhances representational similarity between subjects both within and across datasets; and (iii) boosts one-versus-many decoding of visual stimuli. GLMsingle is a publicly available tool that can significantly improve the quality of past, present, and future neuroimaging datasets that sample brain activity across many experimental conditions.

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bioRxiv2021

The influence of non-neural factors on BOLD signal magnitude

To what extent is the size of the blood-oxygen-level-dependent (BOLD) response influenced by factors other than neural activity? In a re-analysis of three neuroimaging datasets (male and female human participants), we find large systematic inhomogeneities in the BOLD response magnitude in primary visual cortex (V1): stimulus-evoked BOLD responses, expressed in units of percent signal change, are up to 50% larger along the representation of the horizontal meridian than the vertical meridian. To assess whether this surprising effect can be interpreted as differences in local neural activity, we quantified several factors that potentially contribute to the size of the BOLD response. We find relationships between BOLD response magnitude and cortical thickness, curvature, depth and macrovasculature. These relationships are consistently found across subjects and datasets and suggest that variation in BOLD response magnitudes across cortical locations reflects, in part, differences in anatomy and vascularization. To compensate for these factors, we implement a regression-based correction method and show that after correction, BOLD responses become more homogeneous across V1. The correction reduces the horizontal/vertical difference by about half, indicating that some of the difference is likely not due to neural activity differences. We conclude that interpretation of variation in BOLD response magnitude across cortical locations should consider the influence of the potential confounding factors of thickness, curvature, depth and vascularization. Significance statementThe magnitude of the BOLD signal is often used as a surrogate of neural activity, but the exact factors that contribute to its strength have not been studied on a voxel-wise level. Here, we examined several anatomical and measurement-related factors to assess their relationship with BOLD signal magnitude. We find that BOLD magnitude correlates with cortical anatomy, depth and macrovasculature. To remove the contribution of these factors, we propose a simple, data-driven correction method that can be used in any functional magnetic resonance imaging (fMRI) experiment. After accounting for the confounding factors, BOLD magnitude becomes more spatially homogenous. Our correction method improves the ability to make more accurate inferences about local neural activity from fMRI data.

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bioRxiv2021

Short-term plasticity in the visual thalamus

While there is evidence that the visual cortex retains a potential for plasticity in adulthood, less is known about the subcortical stages of visual processing. Here we asked whether short-term ocular dominance plasticity affects the visual thalamus. We addressed this question in normally sighted adult humans, using ultra-high field (7T) magnetic resonance imaging combined with the paradigm of short-term monocular deprivation. With this approach, we previously demonstrated transient shifts of perceptual eye dominance and ocular dominance in visual cortex (Binda et al., 2018). Here we report evidence for short-term plasticity in the ventral division of the pulvinar (vPulv), where the deprived eye representation was enhanced over the non-deprived eye. This pulvinar plasticity effect was similar as previously seen in visual cortex and it was correlated with the ocular dominance shift measured behaviorally. In contrast, there was no short-term plasticity effect in Lateral Geniculate Nucleus (LGN), where results were reliably different from vPulv, despite their spatial proximity. We conclude that the visual thalamus retains potential for short-term plasticity in adulthood; the plasticity effect differs across thalamic subregions, possibly reflecting differences in their cortical connectivity.

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bioRxiv2021

Cross-dataset reproducibility of population receptive field (pRF) estimates and cortical magnification asymmetries

Population receptive field (pRF) models fit to fMRI data are used to non-invasively measure retinotopic maps in human visual cortex, and these maps are a fundamental component of visual neuroscience experiments. Here, we examined the reproducibility of retinotopic maps across two datasets: a newly acquired retinotopy dataset from New York University (NYU) (n=44) and a public dataset from the Human Connectome Project (HCP) (n=181). Our goal was to assess the degree to which pRF properties are similar across datasets, despite substantial differences in their experimental protocols. The two datasets simultaneously differ in their stimulus apertures, participant pool, fMRI protocol, MRI field strength, and preprocessing pipeline. We assessed the cross-dataset reproducibility of the two datasets in terms of the similarity of vertex-wise pRF estimates and in terms of large-scale polar angle asymmetries in cortical magnification. Within V1, V2, V3, and hV4, the group-median NYU and HCP vertex-wise polar angle estimates were nearly identical. Both eccentricity and pRF size estimates were also strongly correlated between the two datasets, but with a slope different from 1; the eccentricity and pRF size estimates were systematically greater in the NYU data. Next, to compare large-scale map properties, we quantified two polar angle asymmetries in V1 cortical magnification previously identified in the HCP data. The NYU dataset confirms earlier reports that more cortical surface area represents horizontal than vertical visual field meridian, and lower than upper vertical visual field meridian. Together, our findings show that the retinotopic properties of V1, V2, V3, and hV4 can be reliably measured across two datasets, despite numerous differences in their experimental design. fMRI-derived retinotopic maps are reproducible because they rely on an explicit computational model of the fMRI response. In the case of pRF mapping, the model is grounded in physiological evidence of how visual receptive fields are organized, allowing one to quantitatively characterize the BOLD signal in terms of stimulus properties (i.e., location and size). The new NYU Retinotopy Dataset will serve as a useful benchmark for testing hypotheses about the organization of visual areas and for comparison to the HCP 7T Retinotopy Dataset.

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bioRxiv2021

An enhanced Bouma model fits a hundred people's visual crowding

AbstractCrowding is the failure to recognize an object due to surrounding clutter. Our visual crowding survey measured 13 crowding distances (or "critical spacings") twice in each of 50 observers. The survey included three eccentricities (0, 5, and 10 deg), four cardinal meridians, two orientations (radial and tangential), and two fonts (Sloan and Pelli). The survey also tested foveal acuity, twice. Remarkably, fitting a two-parameter model, the well- known Bouma law -- crowding distance grows linearly with eccentricity -- explains 82% of the variance for all 13 x 50 measured log crowding distances, cross-validated. An enhanced Bouma law, with factors for meridian, crowding orientation, target kind, and observer, explains 94% of the variance, again cross-validated. These additional factors reveal several asymmetries, consistent with previous reports, which can be expressed as crowding- distance ratios: 0.62 horizontal:vertical, 0.79 lower:upper, 0.78 right:left, 0.55 tangential:radial, and 0.78 Sloan font:Pelli font. Across our observers, peripheral crowding is independent of foveal crowding and acuity. Evaluation of the Bouma factor b (the slope of the Bouma law) as a biomarker of visual health would be easier if there were a way to compare results across crowding studies that use different methods. We define a standardized Bouma factor b that corrects for differences from Boumas 25 choice alternatives, 75% threshold criterion, and linearly symmetric flanker placement. For radial crowding on the right meridian, the standardized Bouma factor b is 0.24 for this study, 0.35 for Bouma (1970), and 0.30 for the geometric mean across five representative modern studies, including this one, showing good agreement across labs, including Boumas. We found that guaranteeing fixation by gaze-contingent display halved the standard deviation across observers of the estimated log b. The reduction in standard deviation is explained by a "peeking" model in which the observer looked near an anticipated target location in 50% of unmonitored-fixation trials. Individual differences are robust, as evidenced by the much larger 0.08 SD of log b across observers than the 0.03 SD of test-retest within observers. Crowdings ease of measurement enhances its promise as a biomarker for dyslexia and visual health.

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bioRxiv2020

The visual white matter connecting human area prostriata and the thalamus is retinotopically organized

The human visual system is capable of processing visual information from fovea to the far peripheral visual field. Recent fMRI studies have shown a full and detailed retinotopic map in area prostriata, located ventro-dorsally and anterior to the calcarine sulcus along the parietooccipital sulcus with strong preference for peripheral and wide-field stimulation. Here, we report the anatomical pattern of white-matter connections between area prostriata and the thalamus encompassing the lateral geniculate nucleus (LGN). We observe a continuous and extended bundle of white matter fibers from which two subcomponents can be extracted: one passing ventrally parallel to the optic radiations (OR) and another passing dorsally circumventing the lateral ventricle. Interestingly, the loop travelling dorsally connects the thalamus with the central visual field representation of prostriata, while the other loop travelling more ventrally connects the LGN with the more peripheral visual field representation. This is consistent with a retinotopic segregation recently demonstrated in the OR, connecting the LGN and V1 in humans. Our results demonstrate for the first time a retinotopic segregation regarding the trajectory of a fiber bundle between the thalamus and an associative visual area.

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bioRxiv2018

Short-term plasticity of 7T BOLD ocular dominance and spatial frequency representation in adult human primary visual cortex

Visual cortex, particularly V1, is considered to be resilient to plastic changes in adults. In particular, ocular dominance is assumed to be hard-wired after the end of the critical period. We show that short-term (2h) monocular deprivation in adult humans boosts the BOLD response to the deprived eye, changing ocular dominance of V1 vertices, consistently with homeostatic plasticity. The boost is strongest in V1, present in V2, V3 & V4 but absent in V3a and MT. Assessment of spatial frequency tuning in V1 by a population Receptive-Field technique shows that deprivation primarily boosts high spatial frequencies, consistent with a primary involvement of the parvocellular pathway. Crucially, the V1 deprivation effect correlates across participants with the perceptual increase of the deprived eye dominance assessed with binocular rivalry, suggesting a common origin. Our results demonstrate that visual cortex, particularly the ventral pathway, retains a high potential for homeostatic plasticity in the human adult.

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