brainlife.io: a decentralized and open-source cloud platform to support neuroscience research.

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.

Serial Dependence in Perception.

Much evidence has shown that perception is biased towards previously presented similar stimuli, an effect recently termed serial dependence. Serial dependence affects nearly every aspect of perception, often causing gross perceptual distortions, especially for weak and ambiguous stimuli. Despite unwanted side-effects, empirical evidence and Bayesian modeling show that serial dependence acts to improve efficiency and is generally beneficial to the system. Consistent with models of predictive coding, the Bayesian priors of serial dependence are generated at high levels of cortical analysis, incorporating much perceptual experience, but feed back to lower sensory areas. These feedback loops may drive oscillations in the alpha range, linked strongly with serial dependence. The discovery of top-down predictive perceptual processes is not new, but the new, more quantitative approach characterizing serial dependence promises to lead to a deeper understanding of predictive perceptual processes and their underlying neural mechanisms.

The functional role of serial dependence.

The world tends to be stable from moment to moment, leading to strong serial correlations in natural scenes. As similar stimuli usually require similar behavioural responses, it is highly likely that the brain has developed strategies to leverage these regularities. A good deal of recent psychophysical evidence is beginning to show that the brain is sensitive to serial correlations, causing strong drifts in observer responses towards previously seen stimuli. However, it is still not clear that this tendency leads to a functional advantage. Here, we test a formal model of optimal serial dependence and show that as predicted, serial dependence in an orientation reproduction task is dependent on current stimulus reliability, with less precise stimuli, such as low spatial frequency oblique Gabors, exhibiting the strongest effects. We also show that serial dependence depends on the similarity between two successive stimuli, again consistent with the behaviour of an ideal observer aiming at minimizing reproduction errors. Lastly, we show that serial dependence leads to faster response times, indicating that the benefits of serial integration go beyond reproduction error. Overall our data show that serial dependence has a beneficial role at various levels of perception, consistent with the idea that the brain exploits the temporal redundancy of the visual scene as an optimization strategy.

Spatiotopic coding during dynamic head tilt.

Humans maintain a stable representation of the visual world effortlessly, despite constant movements of the eyes, head, and body, across multiple planes. Whereas visual stability in the face of saccadic eye movements has been intensely researched, fewer studies have investigated retinal image transformations induced by head movements, especially in the frontal plane. Unlike head rotations in the horizontal and sagittal planes, tilting the head in the frontal plane is only partially counteracted by torsional eye movements and consequently induces a distortion of the retinal image to which we seem to be completely oblivious. One possible mechanism aiding perceptual stability is an active reconstruction of a spatiotopic map of the visual world, anchored in allocentric coordinates. To explore this possibility, we measured the positional motion aftereffect (PMAE; the apparent change in position after adaptation to motion) with head tilts of ∼42° between adaptation and test (to dissociate retinal from allocentric coordinates). The aftereffect was shown to have both a retinotopic and spatiotopic component. When tested with unpatterned Gaussian blobs rather than sinusoidal grating stimuli, the retinotopic component was greatly reduced, whereas the spatiotopic component remained. The results suggest that perceptual stability may be maintained at least partially through mechanisms involving spatiotopic coding.NEW & NOTEWORTHY Given that spatiotopic coding could play a key role in maintaining visual stability, we look for evidence of spatiotopic coding after retinal image transformations caused by head tilt. To this end, we measure the strength of the positional motion aftereffect (PMAE; previously shown to be largely spatiotopic after saccades) after large head tilts. We find that, as with eye movements, the spatial selectivity of the PMAE has a large spatiotopic component after head rotation.

Serial dependencies act directly on perception.

There is good evidence that biological perceptual systems exploit the temporal continuity in the world: When asked to reproduce or rate sequentially presented stimuli (varying in almost any dimension), subjects typically err toward the previous stimulus, exhibiting so-called "serial dependence." At this stage it is unclear whether the serial dependence results from averaging within the perceptual system, or at later stages. Here we demonstrate that strong serial dependencies occur within both perceptual and decision processes, with very little contribution from the response. Using a technique to isolate pure perceptual effects (Fritsche, Mostert, & de Lange, 2017), we show strong serial dependence in orientation judgements, over the range of orientations where theoretical considerations predict the effects to be maximal. In a second experiment we dissociate responses from stimuli to show that serial dependence occurs only between stimuli, not responses. The results show that serial dependence is important for perception, exploiting temporal redundancies to enhance perceptual efficiency.

The oblique effect is both allocentric and egocentric.

Despite continuous movements of the head, humans maintain a stable representation of the visual world, which seems to remain always upright. The mechanisms behind this stability are largely unknown. To gain some insight on how head tilt affects visual perception, we investigate whether a well-known orientation-dependent visual phenomenon, the oblique effect-superior performance for stimuli at cardinal orientations (0° and 90°) compared with oblique orientations (45°)-is anchored in egocentric or allocentric coordinates. To this aim, we measured orientation discrimination thresholds at various orientations for different head positions both in body upright and in supine positions. We report that, in the body upright position, the oblique effect remains anchored in allocentric coordinates irrespective of head position. When lying supine, gravitational effects in the plane orthogonal to gravity are discounted. Under these conditions, the oblique effect was less marked than when upright, and anchored in egocentric coordinates. The results are well explained by a simple "compulsory fusion" model in which the head-based and the gravity-based signals are combined with different weightings (30% and 70%, respectively), even when this leads to reduced sensitivity in orientation discrimination.

Crossing the line: estimations of line length in the Oppel-Kundt illusion.

In the Oppel-Kundt illusion, one of the oldest and least understood geometrical visual illusions, a line subdivided by a series of short orthogonal ticks appears longer than an identical line without these. Paradoxically, bisecting a long line with a single tick leads to perceived shortening of the line. We have systematically investigated the effects of adding 1 to 12 ticks on perceived line length and results suggest that at least three mechanisms must be at work: (a) bisection, which reduces perceived length; (b) a filled extent effect, which is also apparent in the von Helmholtz illusion, though no satisfactory explanation for it exists; and (c) a local contour repulsion effect of the penultimate tick upon the perceived position of the end tick, but this effect, though significant, is too small to explain the Oppel-Kundt illusion in its entirety.

Correction: Visual orientation discrimination skills are tightly linked with specific aspects of human intelligence.

[This corrects the article DOI: 10.1371/journal.pone.0289590.].

Reshaping the peripersonal space in virtual reality.

Peripersonal space (PPS) is defined as the space that lies within reach. Previous research revealed that PPS can be dynamically reshaped with the use of tools extending the arm's reach. Here we investigated whether PPS reshaping depends on the kind of selected tool and/or the motor routine associated with its use. Participants carried out a visuo-tactile detection task in an immersive VR environment that allowed to measure the PPS size before and after a short period of tools use. In Experiment 1, participants had to pull or push objects towards or away from themselves using a shovel. In Experiment 2, they were required to either hammer or shoot an avatar placed in the Extrapersonal space. We found, for the first time in a VR environment, that a period of pull training was effective in enlarging the PPS, a result that replicates and expands previous findings carried out in real life conditions. However, no significant change in PPS size was achieved for training with other tools and motor routines. Our results suggest that the reshaping of PPS is a complex phenomenon in which the kind of interaction between the agent, the targets and the exploited motor routines all play a critical role.

The vertical-horizontal illusion: assessing the contributions of anisotropy, abutting, and crossing to the misperception of simple line stimuli.

Mamassian and de Montalembert (2010) have proposed a simple model of the vertical-horizontal illusion. This model identified two components, an anisotropy which results in horizontal lines being perceived approximately 6% shorter than verticals and a bisection component which results in a bisected line being perceived approximately 16% shorter. We have shown that this bisection component confounds two effects: One when lines cross one another and a second effect when one line abuts another. We propose an extension to the Mamassian-de Montalembert model in which their bisection component is replaced by separate crossing and abutting components.

Visual orientation discrimination skills are tightly linked with specific aspects of human intelligence.

We investigate the notion that basic visual information is acting as a building block for more complex cognitive processes in humans. Specifically, we measured individual visual orientation discrimination thresholds to report significant correlations against the total standardised intelligence quotient (IQ), verbal-IQ and non-verbal IQ scores evaluated using the Wechsler Abbreviated Scale of Intelligence Second Edition (WASI-II) test battery comprising Verbal Reasoning, Block Design, Similarities and Matrix Reasoning subtests (N = 92). A multiple linear regression analysis showed that participants' performance in our visual discrimination task, could be explained only by individual scores in Verbal Reasoning which quantifies the ability to comprehend and describe words and Matrix Reasoning, which evaluates general visual processing skills including abstract and spatial perception. Our results demonstrate that low-level visual abilities and high-level cognitive processes are more tightly interwoven together than previously thought and this result could pave the way for further research on how cognition can be defined by basic sensory processes.

brainlife.io: A decentralized and open source cloud platform to support neuroscience research.

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research.

Perceptual History Acts in World-Centred Coordinates.

Serial dependence effects have been observed using a variety of stimuli and tasks, revealing that the recent past can bias current percepts, leading to increased similarity between two. The aim of this study is to determine whether this temporal integration occurs in egocentric or allocentric coordinates. We asked participants to perform an orientation reproduction task using grating stimuli while the head was kept at a fixed position, or after a 40° yaw rotation between trials, from left (-20°) to right (+20°), putting the egocentric and allocentric cues in conflict. Under these conditions, allocentric cues prevailed.

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 parieto-occipital 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). To this end, we developed and utilized an automated pipeline comprising a series of Apps that run openly on the cloud computing platform brainlife.io to analyse 139 subjects of the Human Connectome Project (HCP). 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 located anteriorly, while the other loop travelling more ventrally connects the LGN with the more peripheral visual field representation located posteriorly. We then analyse an additional cohort of 10 HCP subjects using a manual plane extraction method outside brainlife.io to study the relationship between the two extracted white matter subcomponents and eccentricity, myelin and cortical thickness gradients within prostriata. Our results are consistent with a retinotopic segregation recently demonstrated in the OR, connecting the LGN and V1 in humans and reveal for the first time a retinotopic segregation regarding the trajectory of a fiber bundle between the thalamus and an associative visual area.

Cortical BOLD responses to moderate- and high-speed motion in the human visual cortex.

We investigated the BOLD response of visual cortical and sub-cortical regions to fast drifting motion presented over wide fields, including the far periphery. Stimuli were sinusoidal gratings of 50% contrast moving at moderate and very high speeds (38 and 570 °/s), projected to a large field of view (~60°). Both stimuli generated strong and balanced responses in the lateral geniculate nucleus and the superior colliculus. In visual cortical areas, responses were evaluated at three different eccentricities: central 0-15°; peripheral 20-30°; and extreme peripheral 30-60°. "Ventral stream" areas (V2, V3, V4) preferred moderate-speeds in the central visual field, while motion area MT+ responded equally well to both speeds at all eccentricities. In all other areas and eccentricities BOLD responses were significant and equally strong for both types of moving stimuli. Support vector machine showed that the direction of the fast-speed motion could be successfully decoded from the BOLD response in all visual areas, suggesting that responses are mediated by motion mechanisms rather than being an unspecific preference for fast rate of flicker. The results show that the visual cortex responds to very fast motion, at speeds generated when we move our eyes rapidly, or when moving objects pass by closely.

Area Prostriata in the Human Brain.

Area prostriata is a cortical area at the fundus of the calcarine sulcus, described anatomically in humans [1-5] and other primates [6-9]. It is lightly myelinated and lacks the clearly defined six-layer structure evident throughout the cerebral cortex, with a thinner layer 4 and thicker layer 2 [10], characteristic of limbic cortex [11]. In the marmoset and rhesus monkey, area prostriata has cortical connections with MT+ [12], the cingulate motor cortex [8], the auditory cortex [13], the orbitofrontal cortex, and the frontal polar cortices [14]. Here we use functional magnetic resonance together with a wide-field projection system to study its functional properties in humans. With population receptive field mapping [15], we show that area prostriata has a complete representation of the visual field, clearly distinct from the adjacent area V1. As in the marmoset, the caudal-dorsal border of human prostriata-abutting V1-represents the far peripheral visual field, with eccentricities decreasing toward its rostral boundary. Area prostriata responds strongly to very fast motion, greater than 500°/s. The functional properties of area prostriata suggest that it may serve to alert the brain quickly to fast visual events, particularly in the peripheral visual field.

An Orientation Dependent Size Illusion Is Underpinned by Processing in the Extrastriate Visual Area, LO1.

We use the simple, but prominent Helmholtz's squares illusion in which a vertically striped square appears wider than a horizontally striped square of identical physical dimensions to determine whether functional magnetic resonance imaging (fMRI) BOLD responses in V1 underpin illusions of size. We report that these simple stimuli which differ in only one parameter, orientation, to which V1 neurons are highly selective elicited activity in V1 that followed their physical, not perceived size. To further probe the role of V1 in the illusion and investigate plausible extrastriate visual areas responsible for eliciting the Helmholtz squares illusion, we performed a follow-up transcranial magnetic stimulation (TMS) experiment in which we compared perceptual judgments about the aspect ratio of perceptually identical Helmholtz squares when no TMS was applied against selective stimulation of V1, LO1, or LO2. In agreement with fMRI results, we report that TMS of area V1 does not compromise the strength of the illusion. Only stimulation of area LO1, and not LO2, compromised significantly the strength of the illusion, consistent with previous research that LO1 plays a role in the processing of orientation information. These results demonstrate the involvement of a specific extrastriate area in an illusory percept of size.

Applying the Helmholtz illusion to fashion: horizontal stripes won't make you look fatter.

A square composed of horizontal lines appears taller and narrower than an identical square made up of vertical lines. Reporting this illusion, Hermann von Helmholtz noted that such illusions, in which filled space seems to be larger than unfilled space, were common in everyday life, adding the observation that ladies' frocks with horizontal stripes make the figure look taller. As this assertion runs counter to modern popular belief, we have investigated whether vertical or horizontal stripes on clothing should make the wearer appear taller or fatter. We find that a rectangle of vertical stripes needs to be extended by 7.1% vertically to match the height of a square of horizontal stripes and that a rectangle of horizontal stripes must be made 4.5% wider than a square of vertical stripes to match its perceived width. This illusion holds when the horizontal or vertical lines are on the dress of a line drawing of a woman. We have examined the claim that these effects apply only for 2-dimensional figures in an experiment with 3-D cylinders and find no support for the notion that horizontal lines would be 'fattening' on clothes. Significantly, the illusion persists when the horizontal or vertical lines are on pictures of a real half-body mannequin viewed stereoscopically. All the evidence supports Helmholtz's original assertion.