Biology subjects

Aguirre, G. K.

Publications and source records attributed to Aguirre, G. K..

At least 19 recordsLinked to original sources

bioRxiv2025

Amplifying and ameliorating light avoidance in mice with photoreceptor targeting and CGRP sensitization

ObjectiveTo determine the photoreceptor basis of light avoidance in mice and assess the effect of CGRP sensitization on this behavior. BackgroundPrior studies have suggested that photophobia is mediated by a subset of retinal ganglion cells (RGCs) that contain melanopsin, making them intrinsically photosensitive (ipRGCs). These cells also receive extrinsic input from cones, which can also mediate light sensitivity. Here, we examined whether spectral variation targeting melanopsin or specific cone types in mice could effectively model light sensitivity. Also, we assessed whether sensitizing mice with calcitonin gene-related peptide (CGRP) could amplify ipRGC-mediated light avoidance. MethodsLight avoidance behavior was observed in a two-zone chamber illuminated by narrow-band LEDs targeting photopic opsins: 365 nm (UV; rodent S-cone), 460 nm (blue; melanopsin), and 630 nm (red; human L-cone). In a non-targeted assay, we assessed the degree of light avoidance in wildtype C57BL/6J mice to varying intensities (5 to 100%) of the blue and red LEDs. In a targeted assay, mice were given a choice to spend time between zones with differing relative contrast levels (0.50, 0.75, or 1.00) for the targeted photoreceptor(s). This was assessed in two transgenic mice with: 1) human red cone knock-in (RCKI), or 2) adult-onset ablation of M1 ipRGCs (Opn4aDTA). Mice were studied without intervention or following priming with either peripheral CGRP or vehicle administration every other day for 9 days. A primary measure (mean +/- SEM) was the asymptote value (AV). ResultsWildtype mice showed greater light avoidance with increasing light intensity, demonstrating a parametric response. RCKI mice showed avoidance of the high melanopsin (1.00: 0.52 {+/-} 0.08; n = 18) and L-cone (1.00: 0.30 {+/-} 0.11; n = 15) contrast zones but showed a preference for the higher S-cone (1.00: -0.35 {+/-} 0.06; n = 16) contrast zone. These effects decreased with less relative contrast and, thus, contrast dependent. Adding S-cone contrast opposed avoidance to melanopsin (0.10 {+/-} 0.12; n = 14) or L-cone (-0.19 {+/-} 0.10; n = 15) contrast. Ablation of ipRGCs in Opn4aDTA mice attenuated avoidance of melanopsin and preference for S-cone stimulation compared to control littermates. On day 9, CGRP priming led to significantly increased avoidance of melanopsin stimulation (0.58 {+/-} 0.08, n = 21) as compared to vehicle priming (0.26 {+/-} 0.09, n = 22) (F (1,41) = 5.70, p = 0.02). ConclusionsOur findings further support that ipRGCs play a key role in mediating photophobia. This aversive response to light stems from ipRGCs combining excitatory input from intrinsic melanopsin stimulation and extrinsic L-cone input, which can be opposed by extrinsic inhibitory S-cone input. Chronic exposure to CGRP is likely one of many mechanisms in migraine that can amplify ipRGC signals, leading to photophobia. Plain Language SummaryTo better understand light sensitivity, we studied which cells in the eye cause mice to avoid light. We found that mice avoided blue and red light but preferred UV light, and this is the result of a special cell (ipRGCs) in the eye that combines these light signals. Repeated exposure to CGRP, a key nervous system messenger in migraine, increased avoidance of blue light, which may model what happens in people with chronic migraine who experience light sensitivity.

neuroscience↗

bioRxiv2025

Daily light exposure habits of youth with migraine: A prospective pilot study

BackgroundEighty percent of youth with migraine report photophobia. It is unknown if photophobia leads to light avoidant behavior, and if such behaviors worsen light sensitivity and disrupt sleep. Recently developed wearable, continuous light loggers allow us to address these open questions. We conducted a pilot study to determine the feasibility of measuring light exposure using wearable light loggers in youth with migraine. MethodsYouth 10 - 21 years old with a headache-specialist confirmed ICHD-3 diagnosis of migraine were recruited from CHOP headache clinics. Each participant recorded 7 consecutive days of light logging data from the ActLumus device worn as a pendant around the neck paired with a text-based daily migraine symptom diary during a typical school week between November and March 2024. Validated questionnaires were used to capture any headache and bad headache frequency, headache-related disability, visual sensitivity, fear-of-pain, and sleep disturbance and impairment. Percent time spent within recommended light exposure levels was calculated for the day, 3 hours prior to bedtime, and night. Power analysis was calculated to determine sample size needed for group comparison of baseline characteristics across light intensity and light timing metrics to aid in the design of larger studies. ResultsTwenty youth with a median age 17 years [IQR 16, 19], 70% of whom were female completed 7 days of continuous light logger recording and daily headache diary. Data completion rates were high with 136/140 (97.1%) useable days of light logger data, and 100% compliance on the daily headache diary. Participant feedback on the study was positive; 85% would recommend the study to others. On average, participants received recommended light exposure during only 14.5% +/- SD 7.0 of daylight hours. By contrast, participants were more consistently below the recommended maximum light levels 3 hours prior to bed (77.5% +/- 21.6 of the time), and at night (99.1% +/- 2.9 of the time). Youth with chronic migraine (i.e., at least 15 headache days and 8 bad headache days per month) had daily light exposure patterns that were phase shifted 60 minutes later as compared to participants with non-chronic migraine. Power analyses suggest that future tests for differences in light exposure between migraine-characteristic groups (e.g., differing by headache frequency, severity, or disability) will require sample sizes on the order of 50 to 150 to reach 80% power with an alpha of 0.05. ConclusionMeasuring daily light exposure is feasible in pediatric populations with photophobia and reveals intriguing trends in youth with migraine that warrant further study.

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bioRxiv2024

The tilt illusion arises from an efficient reallocation of neural coding resources at the contextual boundary

The tilt illusion -- a bias in the perceived orientation of a center stimulus induced by an oriented surround -- illustrates how context shapes visual perception. While the tilt illusion has been the subject of quantitative study for over 85 years, we still lack a comprehensive account of the phenomenon that connects its neural and behavioral characteristics. Here, we demonstrate that the tilt illusion originates from a dynamic change in neural coding precision induced by the surround context. We simultaneously obtained psychophysical and fMRI responses from human subjects while they viewed gratings in the absence and presence of an oriented surround, and extracted sensory encoding precision from their behavioral and neural data. Both measures show that in the absence of a surround, encoding reflects the natural scene statistics of orientation. However, in the presence of an oriented surround, encoding precision is significantly increased for stimuli similar to the surround orientation. This local change in encoding is sufficient to accurately predict the behavioral characteristics of the tilt illusion using a Bayesian observer model. The effect of surround modulation increases along the ventral stream, and is localized to the portion of the visual cortex with receptive fields at the center-surround boundary. The pattern of change in coding accuracy reflects the surround-conditioned orientation statistics in natural scenes, but cannot be explained by local stimulus configuration. Our results suggest that the tilt illusion naturally emerges from a dynamic coding strategy that efficiently reallocates neural coding resources based on the current stimulus context.

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bioRxiv2024

Neural compass in the human brain during naturalistic virtual navigation

A central component of wayfinding is the ability to maintain a consistent representation of ones facing direction when moving about the world. In rodents, head direction cells are believed to support this "neural compass", but identifying a similar mechanism in humans during dynamic naturalistic navigation has been challenging. To address this issue, we acquired fMRI data while participants freely navigated through a virtual reality city. Encoding model analyses revealed voxel clusters in retrosplenial complex and superior parietal lobule that exhibited reliable tuning as a function of facing direction. Crucially, these directional tunings were consistent across perceptually different versions of the city, spatially separated locations within the city, and motivationally distinct phases of the behavioral task. Analysis of the model weights indicated that these regions may represent facing direction relative to the principal axis of the environment. These findings reveal specific mechanisms in the human brain that allow us to maintain a sense of direction during naturalistic, dynamic navigation.

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bioRxiv2024

Temporal dynamics of human color processing measured using a continuous tracking task

We characterized the temporal dynamics of color processing using a continuous tracking paradigm by estimating temporal impulse response functions associated with tracking chromatic Gabor patches. We measured how the lag of these functions changes as a function of chromatic direction and contrast for stimuli in the LS cone contrast plane. In the same set of subjects, we also measured detection thresholds for stimuli with matched spatial, temporal, and chromatic properties. We created a model of tracking and detection performance to test if a common representation of chromatic contrast accounts for both measures. The model summarizes the effect of chromatic contrast over different chromatic directions through elliptical isoresponse contours, the shapes of which are contrast independent. The fitted elliptical isoresponse contours have essentially the same orientation in the detection and tracking tasks. For the tracking task, however, there is a striking reduction in sensitivity to signals originating in the S cones. The results are consistent with common chromatic mechanisms mediating performance on the two tasks, but with task-dependent relative weighting of signals from L and S cones.

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bioRxiv2023

Cone-driven, geniculo-cortical responses in canine models of outer retinal disease

PurposeCanine models of inherited retinal degeneration are used for proof-of-concept of emerging gene and cell-based therapies that aim to produce functional restoration of cone-mediated vision. We examined functional MRI measures of the post-retinal response to cone-directed stimulation in wild type (WT) dogs, and in three different retinal disease models. MethodsTemporal spectral modulation of a uniform field of light around a photopic background was used to target the canine L/M (hereafter "L") and S cones and rods. Stimuli were designed to separately target the post-receptoral luminance (L+S) and chrominance (L-S) pathways, the rods, and all photoreceptors jointly (light flux). These stimuli were presented to WT, and mutant PDE6B-RCD1, RPGR-XLPRA2, and NPHP5-CRD2 dogs during pupillometry and fMRI. ResultsPupil responses in WT dogs to light flux, L+S, and rod-directed stimuli were consistent with responses being driven by cone signals alone. For WT animals, both luminance and chromatic (L-S) stimuli evoked fMRI responses in the lateral geniculate nucleus (LGN) or visual cortex; RCD1 animals with predominant rod loss had similar responses. Responses to cone-directed stimulation were reduced in XLPRA2 and absent in CRD2. NPHP5 gene augmentation restored the cortical response to luminance stimulation in a CRD2 animal. ConclusionsCone-directed stimulation during fMRI can be used to measure the integrity of luminance and chrominance responses in the dog visual system. The NPHP5-CRD2 model is appealing for studies of recovered cone function. Translational RelevancefMRI assessment of cone driven cortical response provides a tool to translate cell/gene therapies for vision restoration.

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bioRxiv2023

Temporal sensitivity for achromatic and chromatic flicker across the visual cortex

The retinal ganglion cells (RGCs) receive different combinations of L, M, and S cone inputs and give rise to one achromatic and two chromatic post-receptoral channels. Beyond the retina, RGC outputs are subject to filtering and normalization along the geniculo-striate pathway, ultimately producing the properties of human vision. The goal of the current study was to determine temporal sensitivity across the three post-receptoral channels in subcortical and cortical regions involved in vision. We measured functional magnetic resonance imaging (MRI) responses at 7 Tesla from three participants (two males, one female) viewing a high-contrast, flickering, spatially-uniform wide field (~140{degrees}). Stimulus flicker frequency varied logarithmically between 2 and 64 Hz and targeted the L+M+S, L-M, and S-[L+M] cone combinations. These measurements were used to create temporal sensitivity functions of primary visual cortex (V1) across eccentricity, and spatially averaged responses from lateral geniculate nucleus (LGN), V2/V3, hV4, and V3A/B. Functional MRI responses reflected known properties of the visual system, including higher peak temporal sensitivity to achromatic vs. chromatic stimuli, and low-pass filtering between the LGN and V1. Peak temporal sensitivity increased across levels of the cortical visual hierarchy. Unexpectedly, peak temporal sensitivity varied little across eccentricity within area V1. Measures of adaptation and distributed pattern activity revealed a subtle influence of 64 Hz achromatic flicker in area V1, despite this stimulus evoking only a minimal overall response. Comparison of measured cortical responses to a model of integrated retinal output to our stimuli demonstrates that extensive filtering and amplification is applied to post-retinal signals. Significance StatementWe report the temporal sensitivity of human visual cortex across the three canonical post-receptoral channels from central vision to the far periphery. Functional MRI measurements of responses from the LGN, V1, and higher visual cortical areas demonstrate modification of temporal sensitivity across the visual hierarchy. This includes amplification of chromatic signals between the LGN and V1, and an increase in peak temporal sensitivity in visual areas beyond V1. Within V1, we find a surprising stability of peak temporal sensitivity in the periphery for all three post-receptoral directions. Comparison of our results to a model of retinal output demonstrates the presence of substantial post-retinal filtering, yielding greater uniformity of responses across area V1 than would be predicted from unmodified retinal signals.

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bioRxiv2023

Network structure influences the strength of learned neural representations

Human experience is built upon sequences of discrete events. From those sequences, humans build impressively accurate models of their world. This process has been referred to as graph learning, a form of structure learning in which the mental model encodes the graph of event-to-event transition probabilities [1], [2], typically in medial temporal cortex [3]-[6]. Recent evidence suggests that some network structures are easier to learn than others [7]-[9], but the neural properties of this effect remain unknown. Here we use fMRI to show that the network structure of a temporal sequence of stimuli influences the fidelity with which those stimuli are represented in the brain. Healthy adult human participants learned a set of stimulus-motor associations following one of two graph structures. The design of our experiment allowed us to separate regional sensitivity to the structural, stimulus, and motor response components of the task. As expected, whereas the motor response could be decoded from neural representations in postcentral gyrus, the shape of the stimulus could be decoded from lateral occipital cortex. The structure of the graph impacted the nature of neural representations: when the graph was modular as opposed to lattice-like, BOLD representations in visual areas better predicted trial identity in a held-out run and displayed higher intrinsic dimensionality. Our results demonstrate that even over relatively short timescales, graph structure determines the fidelity of event representations as well as the dimensionality of the space in which those representations are encoded. More broadly, our study shows that network context influences the strength of learned neural representations, motivating future work in the design, optimization, and adaptation of network contexts for distinct types of learning over different timescales.

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bioRxiv2022

Parametric modulation of the blink reflex provides an individual difference measure of trigeminal sensitivity

The primary goal of this study was to develop a parametric model that relates variation in stimulation of the trigeminal nerve to properties of the blink response. We measured blink responses in 17 healthy, adult participants to air puffs directed at the lateral canthus of the eye at five different, log-spaced intensities (3.5 - 60 PSI). Lid position over time was decomposed into amplitude and velocity components. We found that blink amplitude was systematically related to log stimulus intensity, with the relationship well described by a sigmoidal function. The parameters of the model fit correspond to the slope of the function and the stimulus intensity required to produce half of a maximal blink response (the half-response threshold). There was a reliable decrease in the half-response threshold for the contralateral as compared to the ipsilateral blink response. This decrease was consistent across participants despite substantial individual differences in the half-response threshold and slope parameters of the overall sensitivity function, suggesting that the laterality effect arises in the neural circuit subsequent to individual differences in sensitivity. Overall, we find that graded mechanical stimulation of the somatosensory trigeminal afferents elicits a graded response that is well described by a simple parametric model. We discuss the application of parametric measurements of the blink response to the detection of group differences in trigeminal sensitivity. Impact statementO_LIThere has been limited study of how variation in stimulus intensity influences the cutaneous blink response. We describe how variation in the intensity of an air-puff stimulus relates to the amplitude of the blink response using a two-parameter model. The parameters of the model capture individual differences in response, which may be used in future studies to identify population differences in trigeminal sensitivity. C_LI

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bioRxiv2022

Retinal ganglion cell endowment is correlated with optic tract fiber cross section, not density

There is substantial variation between healthy individuals in the number of retinal ganglion cells (RGC) in the eye, with commensurate variation in the number of axons in the optic tracts. Fixel-based analysis of diffusion MR produces estimates of fiber density (FD) and cross section (FC). Using these fixel measurements along with retinal imaging, we asked if individual differences in RGC tissue volume are correlated with individual differences in FD and FC measurements obtained from the optic tracts, and subsequent structures along the cortical visual pathway. We find that RGC endowment is correlated with optic tract FC, but not with FD. RGC volume had a decreasing relationship with measurements from subsequent regions of the visual system (LGN volume, optic radiation FC/FD, and V1 surface area). However, we also found that the variations in each visual area were correlated with the variations in its immediately adjacent visual structure. We only observed these serial correlations when FC is used as the measure of interest for the optic tract and radiations, but no significant relationship was found when FD represented these white matter structures. From these results, we conclude that the variations in RGC endowment, LGN volume, and V1 surface area are better predicted by the overall cross section of the optic tract and optic radiations as compare to the intra-axonal restricted signal component of these white matter pathways. Additionally, the presence of significant correlations between adjacent, but not distant, anatomical structures suggests that there are multiple, local sources of anatomical variation along the visual pathway.

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bioRxiv2022

Persistent horizontal and vertical, MR-induced nystagmus in resting state Human Connectome Project data

ObjectiveStrong magnetic fields from magnetic resonance (MR) scanners induce a Lorentz force that contributes to vertigo and persistent nystagmus. Prior studies have reported a predominantly horizontal direction for healthy subjects in a 7 Tesla (T) MR scanner, with slow phase velocity (SPV) dependent on head orientation. Less is known about vestibular signal behavior for subjects in a weaker, 3T magnetic field, the standard strength used in the Human Connectome Project (HCP). The purpose of this study is to characterize the form and magnitude of nystagmus induced at 3T. MethodsForty-two subjects were studied after being introduced head-first, supine into a Siemens Prisma 3T scanner. Eye movements were recorded in four separate acquisitions over 20 minutes. A biometric eye model was fit to the recordings to derive rotational eye position and then SPV. An anatomical template of the semi-circular canals was fit to the T2 anatomical image from each subject, and used to derive the angle of the B0 magnetic field with respect to the vestibular apparatus. ResultsRecordings from 37 subjects yielded valid measures of eye movements. The population-mean SPV {+/-} SD for the horizontal component was -1.38 {+/-} 1.27 deg/sec, and vertical component was -0.93 {+/-} 1.44 deg/sec, corresponding to drift movement in the rightward and downward direction. Although there was substantial inter-subject variability, persistent nystagmus was present in half of subjects with no significant adaptation over the 20 minute scanning period. The amplitude of vertical drift was correlated with the roll angle of the vestibular system, with a non-zero vertical SPV present at a 0 degree roll. InterpretationNon-habituating vestibular signals of varying amplitude are present in resting state data collected at 3T.

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bioRxiv2021

Melanopic stimulation does not affect psychophysical threshold sensitivity for luminance flicker

In addition to the cone photoreceptors the retina contains intrinsically photosensitive retinal ganglion cells (ipRGCs). These cells express the photopigment melanopsin and are known to be involved in reflexive visual functions such as pupil response and photo-entrainment of the circadian rhythm. It is possible that the ipRGCs contribute to conscious visual perception, either by providing an independent signal to the geniculo-striate pathway, or by interacting with and thus modifying signals arising from "classical" retinal ganglion cells that combine and contrast cone input. Here, we tested for the existence of an interaction by asking if a 350% change in melanopsin stimulation alters psychophysical sensitivity for the detection of luminance flicker. In Experiment 1, we tested for a change in the threshold for detecting luminance flicker in three participants after they adapted to backgrounds with different degrees of tonic melanopsin stimulation. In Experiments 2 and 3, this test was repeated, but now for luminance flicker presented on a transient pedestal of melanopsin stimulation. Across the three experiments, no effect of melanopsin stimulation upon threshold flicker sensitivity was found. Our results suggest that even large changes in melanopsin stimulation do not affect near-threshold, cone-mediated visual perception.

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bioRxiv2021

FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

The recent and growing focus on reproducibility in neuroimaging studies has led many major academic centers to use cloud-based imaging databases for storing, analyzing, and sharing complex imaging data. Flywheel is one such database platform that offers easily accessible, large-scale data management, along with a framework for reproducible analyses through containerized pipelines. The Brain Imaging Data Structure (BIDS) is a data storage specification for neuroimaging data, but curating neuroimaging data into BIDS can be a challenging and time-consuming task. In particular, standard solutions for BIDS curation are not designed for use on cloud-based systems such as Flywheel. To address these challenges, we developed "FlywheelTools", a software toolbox for reproducible data curation and manipulation on Flywheel. FlywheelTools includes two elements: fw-heudiconv, for heuristic-driven curation of data into BIDS, and flaudit, which audits and inventories projects on Flywheel. Together, these tools accelerate reproducible neuroscience research on the widely used Flywheel platform.

bioinformatics↗

bioRxiv2021

A model of the appearance of the moving human eye

The entrance pupil and first Purkinje reflection ("glint") in an image of the human eye serve as important features in 3D, model-based eye tracking applications. Here I present a physically and biologically accurate, ray-traced model that supplies the appearance of the pupil and glint of a moving eye. Once biometrically calibrated for a subject under study, simultaneous fitting of the pupil and glint features by the model supplies eye rotation, radius of the aperture stop, and the translation of the eye relative to the initial camera position. The biometric parameters of the model, including corneal curvature and the depth of the centers of rotation, are obtained by model-based fitting of images of the eye posed at known gaze angles. This approach was applied to eye recordings from 30 people obtained during gaze calibration, and while head position was recorded simultaneously using echoplanar magnetic resonance imaging. The refractive and reflective effects of spectacle and contact lenses worn by some subjects were incorporated into the model. The fitted parameters reveal that the center of rotation for horizontal eye movements is deeper (13.8 mm) than that for vertical eye movements (12.1) mm, consistent with prior studies. Individual differences in the depth of the rotation centers, and in corneal curvature, were well related to biometric measures obtained from these subjects using clinical ophthalmologic instruments. Once biometrically calibrated for each subject, gaze position was modeled with a cross-validated, median (across subject) absolute error of 0.58{degrees}, and image-plane translation of the head was estimated with sub-millimeter accuracy. The open-source model described here produces biologically accurate simulations of the appearance of the eye in motion, and may be used in model-based search to derive eye pose and biometric properties from empirical data.

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bioRxiv2020

Enhanced reflexive eye closure is mediated by ipRGC signals and is specific to migraine with visual aura

ObjectiveTo assess the contribution of the melanopsin-containing, intrinsically photosensitive retinal ganglion cells (ipRGCs) and the cones to reflexive eye closure as an implicit measure of interictal photophobia in migraine. MethodsWe studied twenty participants in each of three groups: headache-free (HAf) controls, migraine without aura (MwoA), and migraine with visual aura (MwA). Participants viewed spectral pulses that selectively targeted melanopsin, the cones, or their combination while we recorded orbicularis oculi electromyography (OO-EMG) and blinking rate. ResultsTime course analysis of OO-EMG demonstrated that reflexive eye closure was tightly coupled to the spectral pulses. Compared to both the MwoA and HAf control groups, the MwA group had enhanced OO-EMG and blinking activity in response to melanopsin and cone stimulation in combination and in isolation. This response scaled with the contrast of the stimulus. ConclusionsOur findings suggest that ipRGC signals, whether elicited by melanopsin stimulation or from presumed extrinsic cone input, provide the afferent input for light-induced reflexive eye closure in a photophobic state. Participants with migraine and visual aura had a distinctly different response to visual stimulation as compared to the other two groups. This is in contrast to prior findings in this same cohort in whom higher explicit ratings of visual discomfort were found for both MwA and MwoA as compared to controls. Such a dissociation suggests distinct pathophysiology in forms of migraine, interacting with separate neural pathways by which ipRGC signals elicit implicit and explicit signs of visual discomfort.

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bioRxiv2020

A Quadratic Model Captures the Human V1 Response to Variations in Chromatic Direction and Contrast

An important goal for vision science is to develop quantitative models for the representation of visual signals at post-receptoral sites. To this end, we develop the quadratic color model (QCM) and examine its ability to account for the BOLD fMRI response in human V1 to spatially-uniform temporal chromatic modulations, systematically varying in their chromatic directions and contrasts. We find that the QCM explains the same, cross-validated variance as a conventional GLM, with far fewer free parameters. The QCM generalizes to allow prediction of V1 responses to a large range of modulations. We replicated the results for each subject and find good agreement across both replications and subjects. We find that within the LM cone contrast plane, V1 is most sensitive to L-M contrast modulations and least sensitive to L+M contrast modulations. Within V1, we observe little to no change in chromatic sensitivity as a function of eccentricity.

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bioRxiv2020

QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI

Diffusion-weighted magnetic resonance imaging (dMRI) has become the primary method for non-invasively studying the organization of white matter in the human brain. While many dMRI acquisition sequences have been developed, they all sample q-space in order to characterize water diffusion. Numerous software platforms have been developed for processing dMRI data, but most work on only a subset of sampling schemes or implement only parts of the processing workflow. Reproducible research and comparisons across dMRI methods are hindered by incompatible software, diverse file formats, and inconsistent naming conventions. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing upon a diverse set of software suites to capitalize upon their complementary strengths, QSIPrep automatically applies best practices for dMRI preprocessing, including denoising, distortion correction, head motion correction, coregistration, and spatial normalization. Throughout, QSIPrep provides both visual and quantitative measures of data quality as well as "glass-box" methods reporting. Taken together, these features facilitate easy implementation of best practices for processing of diffusion images while simultaneously ensuring reproducibility.

bioinformatics↗

bioRxiv2020

The influence of axial length upon the retinal ganglion cell layer of the human eye

PurposeWe examined the relationship between axial length and the thickness and volume of the ganglion cell layer (GCL) of the retina, and related these measures to the size of the optic chiasm. MethodsWe used optical coherence tomography to measure the thickness of the GCL over a 50{degrees} extent of the horizontal meridian in 50 normally-sighted participants with a wide range of axial lengths. Using a model eye informed by individual biometry, we converted GCL thickness to tissue volume per square degree. The volume of the optic chiasm was measured for 40 participants using magnetic resonance imaging. ResultsWhile GCL thickness decreases with increasing axial length, there is a positive relationship between GCL tissue volume and axial length, leading us to conclude that increasing axial length is associated with decreased retinal ganglion cell packing, increased cell size, or both. We characterize how retinal ganglion cell tissue varies systematically in volume and spatial distribution as a function of axial length. This model allows us to remove the effect of axial length from individual difference measures of GCL volume. We find that variation in GCL volume correlates well with the size of the optic chiasm as measured using magnetic resonance imaging. ConclusionsOur results provide the volume of ganglion cell tissue in the retina, adjusted for the effects of axial length upon ganglion cell size and/or packing. The resulting volume measure accounts for individual differences in the size of the optic chiasm, supporting its use to characterize the post-retinal visual pathway.

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