Bas Rokers’s research while affiliated with New York University Abu Dhabi and other places

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Publications (88)


Fig. 1. Distribution of cortical thickness (CT), curvature (CV) and T1-w signal intensity across participants. A -Left: Violin plot showing CT, CV and T1-w signal for normally sighted controls (NSC) and congenital cataract reversal (CC) individuals, using the raw data. A -Right: lateral and medial brain surface representing the mean T1-w signal intensity for CC and NSC, using the raw data. B -Left: Violin plot showing standardized values of CT, CV and T1-w signal for CC and NSC. B -Right: lateral and medial brain surface representing the mean standardized T1-w signal intensity for CC and NSC.
Fig. 2. Effect of group at whole brain level. Cold colors represent z-scores greater in normally sighted controls (NSC); warm colors represent z-scores greater in congenital cataract-reversal (CC) participants. Results are shown after applying different levels of smoothing. Results are significant after cluster correction (vertex-wise cluster threshold of 3 and a cluster-wise p-threshold set to 0.05). CC individuals show greater T1-w signal and thicker thickness in occipital and callosal cortex, compared to NSC.
Fig. 4. Effect of time since surgery at ROI-level in the group of individuals who have been treated for dense bilateral congenital cataract. Lateral and medial brain surface superimposed with the Desikan-Killiany Atlas. Each plot represents z-scores T1-w signal, cortical thickness or curvature for each subject as a function of time since surgery. Each color represents a CC individual and each line is connecting the multiple timepoints from the same subject. The dashed line indicates the beta extracted from the linear mixed-effect model, with the
Gray matter abnormalities in sight deprivation and sight restoration
  • Preprint
  • File available

November 2024

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19 Reads

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Alessio Fracasso

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Amna Dogar

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[...]

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Blindness provides a unique model for investigating brain plasticity in response to sensory deprivation. While structural changes in both gray and white matter have been widely documented, particularly in cases of early or congenital visual deprivation, gray matter studies have traditionally focused on cortical thickness, often finding cortical thickening in posterior regions. However, other aspects of gray matter integrity, such as cortical myelin content, remain underexplored. In this study, we examined the effects of visual deprivation on cortical structure in a cohort of congenitally blind individuals who received eye surgery during adolescence, expanding beyond conventional measures to include cortical thickness, curvature, and T1-weighted signal intensity. This multi-faceted approach offers a more comprehensive view of cortical adaptations to congenital sensory deprivation. While blindness offers valuable insights into sensory-driven brain plasticity, an intriguing and unresolved question is whether structural plasticity reverses after sight restoration, enabling typical visual processing circuits to develop despite the initial period of deprivation. To address this, we assessed the effect of sight-recovering eye surgery on gray matter changes. Critically, individuals in this cohort received surgery after the closure of the sensitive period for visual development. We did not find evidence of gray matter changes after surgery. However, in a previous study conducted on the same cohort, we reported that notable plasticity in white matter emerged in this same population. These results suggest that white matter alterations, rather than gray matter changes, may potentially serve as a biomarker of structural plasticity following sight restoration, even beyond the sensitive developmental window.

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Figure 1. Choice of the model size. Visualization of the criteria used to select the order of the HMM. A: Visualization of Gamma (upper), Viterbi Path (middle) and transition probability (bottom) for one subject from Dataset 2. B. Multiple measures extracted from each model order: Coefficient of Variation, as a measure of reliability of mean estimates as the model order increases; Mean Correlation, Geodesic Distance and Pearson Dissimilarity as measures of independence of hidden states.
Figure 4. Maps of mean activation estimated from HMM using different numbers of states (from 5 to 9). Dashed red squares indicate significant results. The blue dashed square indicates the chosen model order.
Characterizing dynamic functional connectivity in congenitally blind people using Hidden Markov Models

October 2024

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41 Reads

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1 Citation

How does sensory experience influence the brain connectome? Early acquired blindness is known to trigger a large-scale alteration in brain connectivity. Previous studies have traditionally assessed stationary functional connectivity across all timepoints in scanning sessions. In this study we compared the dynamic nature of functional connectivity in sighted (50) and early/congenitally blind (33) individuals through the data-driven approach of Hidden Markov Models (HMM). Blind individuals showed increased fractional occupancy in two key brain states: one characterized by bilateral somatomotor activation and another by occipito-frontal activation, mainly in the left hemisphere. Conversely, sighted individuals more frequently occupied a state associated with Default Mode and Ventral Attentional networks. Network analysis revealed decreased connectivity in blind individuals within states frequently occupied by sighted individuals, particularly between visual and somatomotor regions. In contrast, states more often visited by blind individuals exhibited increased connectivity within the visual network, connecting multiple occipital regions with the temporal fusiform area, as well as between visual and prefrontal regions. These results suggest that the frequency of visiting specific brain states may contribute to the differences observed between blind and sighted individuals in stationary resting state functional connectivity. Together, these findings show the effectiveness of Hidden Markov Models in capturing the temporal dynamics of functional connectivity, revealing its variability over time. We found that early visual deprivation disrupts these dynamics, with blindness leading to prolonged activation of unimodal regions and increased connectivity within the visual network and between occipital and higher-order brain regions. Additionally, alterations in the chronnectome, defined as the functional connectome changing over time - specifically in the time spent visiting a state - may provide new insights into stationary functional connectivity patterns in blind individuals, establishing a foundation for understanding network connectivity dynamics following sensory deprivation.


Figure 2. Delinea�ng pFST. (A) Poten�al rela�onships between mo�on localizers and mo�on-processing areas. (B) drawing pFST in different scenarios based on the ac�va�on of 2D-and 3D-mo�on localizers. Blue patch represents selec�vity to 2D mo�on,
Figure 3. Loca�on of area pFST and hMT/MST across individual hemispheres on the white and pial surface as well as in a glass-brain view. Each row represents a separate par�cipant. The blue area represents hMT/MST and the red area represents pFST.
Figure 4. Results across 8 measures in an example hemisphere. hMT/MST is labeled with a blue outline and area pFST is labeled with a red outline. [le�, first row] 2D-mo�on response (2D moving -sta�c dots), [le�, second row] 3D-mo�on response (coherent stereomo�on -temporally scrambled dots w/disparity), and [le�, third row] mo�on opponency (unpaired -paired moving dots) thresholded at the 90 th percen�le. [le�, fourth row] R1 rate (1/T1). Higher values are associated with greater myelin density. In the dot plot each dot represents a single vertex from the surface and each line connects each of the 10 th percen�les of the distribu�on across the two ROIs. Nega�ve slopes (hMT/MST > pFST) are colored blue, and posi�ve slopes are colored orange. [right, first to fourth rows] Es�mated pRF parameters: variance explained (R 2 ), eccentricity (deg), pRF size (deg), and polar angle (angle 0-360). All pRF results are thresholded at R 2 > 10%.
Figure 5. Re�notopic mapping differen�ates hMT/MST and pFST. (A) Variance explained for one subject, using the pRF model versus s�mulus contrast (ON/OFF) model in V1, hMT/MST, and pFST. (B-C) pRF size and eccentricity are underes�mated for large pRFS, especially with low signal-to-noise (SNR). Error bars represent the standard error across bootstrap simula�ons.
Figure 7. Func�onal vs. atlas-defined pFST. (A) Func�onal and atlas-defined ROIs in na�ve inflated-surface space. Each cluster represents the overlap of regions delineated based on an atlas (Glasser et al., 2016) vs. func�onal localizer within a single hemisphere. Atlas-defined hMT and MST are combined into one ROI, which is comparable with func�onally defined hMT/MST. Color-filled areas indicate ver�ces from ROIs manually drawn based on our localiza�on criteria (2D-and 3D-mo�on func�onal localizers). Atlas-defined ROIs are shown as unfilled outlines. For both func�onal and atlas-defined ROIs, hMT/MST is filled in blue while pFST is filled in red. Filled areas with semi-transparent blue/red color indicate ver�ces that have consistent ROI labels for atlas-and func�onally defined methods. (B) Surface area overlap (%): The bar plot shows the mean overlap percentage ± 1 standard error (black ver�cal line) across hemispheres in na�ve space. Red circles mark the mean overlap value across subjects in fsaverage space. (C) Surface distance (cm): Distances in cen�meters are calculated between the centroid coordinates of each ROI in inflated-surface space, with red circles marking the mean distance in fsaverage space. (D) Surface area (mm 2 ): Mean surface area of func�onally defined ROIs in inflated-surface space, with red circles marking the mean area of averaged func�onally defined ROIs in fsaverage space.
Functional localization of visual motion area FST in humans

September 2024

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36 Reads

The fundus of the superior temporal sulcus (FST) in macaques is implicated in the processing of complex motion signals, yet a human homolog remains elusive. Here we considered potential localizers and evaluated their effectiveness in delineating putative FST (pFST), from hMT and MST, two nearby motion-sensitive areas in humans. Nine healthy participants underwent scanning sessions with 2D and 3D motion localizers, as well as population receptive field (pRF) mapping. We observed consistent anterior and inferior activation relative to hMT and MST in response to stimuli that contained coherent 3D, but not 2D, motion. Motion opponency and myelination measures further validated the functional and structural distinction between pFST and hMT/MST. At the same time, standard pRF mapping techniques that reveal the visual field organization of hMT/MST proved suboptimal for delineating pFST. Our findings provide a robust framework for localizing pFST in humans, and underscore its distinct functional role in motion processing.






Tracts in the limbic system show microstructural alterations post COVID-19 recovery

May 2024

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49 Reads

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1 Citation

Brain Communications

Delirium, memory loss, attention deficit and fatigue are frequently reported by COVID survivors, yet the neurological pathways underlying these symptoms are not well understood. To study the possible mechanisms for these long-term sequelae after COVID-19 recovery, we investigated the microstructural properties of white matter in Indian cohorts of COVID-recovered patients and healthy controls. For the cross-sectional study presented here, we recruited 44 COVID-recovered patients and 29 healthy controls in New Delhi, India. Using deterministic whole-brain tractography on the acquired diffusion MRI scans, we traced 20 white matter tracts and compared fractional anisotropy, axial, mean and radial diffusivity between the cohorts. Our results revealed statistically significant differences (PFWE < 0.01) in the uncinate fasciculus, cingulum cingulate, cingulum hippocampus and arcuate fasciculus in COVID survivors, suggesting the presence of microstructural abnormalities. Additionally, in a subsequent subgroup analysis based on infection severity (healthy control, non-hospitalized patients and hospitalized patients), we observed a correlation between tract diffusion measures and COVID-19 infection severity. Although there were significant differences between healthy controls and infected groups, we found no significant differences between hospitalized and non-hospitalized COVID patients. Notably, the identified tracts are part of the limbic system and orbitofrontal cortex, indicating microstructural differences in neural circuits associated with memory and emotion. The observed white matter alterations in the limbic system resonate strongly with the functional deficits reported in Long COVID. Overall, our study provides additional evidence that damage to the limbic system could be a neuroimaging signature of Long COVID. The findings identify targets for follow-up studies investigating the long-term physiological and psychological impact of COVID-19.


Hierarchical computation of 3D motion across macaque areas MT and FST

December 2023

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29 Reads

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3 Citations

Cell Reports

Computing behaviorally relevant representations of three-dimensional (3D) motion from two-dimensional (2D) retinal signals is critical for survival. To ascertain where and how the primate visual system performs this computation, we recorded from the macaque middle temporal (MT) area and its downstream target, the fundus of the superior temporal sulcus (area FST). Area MT is a key site of 2D motion processing, but its role in 3D motion processing is controversial. The functions of FST remain highly underexplored. To distinguish representations of 3D motion from those of 2D retinal motion, we contrast responses to multiple motion cues during a motion discrimination task. The results reveal a hierarchical transformation whereby many FST but not MT neurons are selective for 3D motion. Modeling results further show how generalized, cue-invariant representations of 3D motion in FST may be created by selectively integrating the output of 2D motion selective MT neurons.


Fig. S2. All-trial analysis of target contrast effects on serial dependence. (a.) Left: Serial dependence curves and DoG fits to error data from all trials when no feedback was provided (green), when auditory feedback was provided (red), and when auditory + visual feedback was provided (blue), sorted according to the relative direction of the current trial's target with respect to the previous trial's target direction and split out by current trial target contrast. Shaded bands represent +/-1 SEM. **corresponds to bootstrapped p-values < .001; n.s. = non-significant; pvalues at the bottom of each graph refer to the difference in amplitude parameter between no feedback and auditory feedback groups (red font) and between no feedback and auditory + visual feedback groups (blue font) derived from permutation testing. Right: Model-free serial bias with respect to the previous trial's target direction for the three feedback conditions, split out by current trial target contrast. Circular symbols correspond to individual subject biases; black symbols correspond to group means. Error bars represent +/-1 SEM. *corresponds to pvalues < .05 (b.) Same formats as (a.) split according to previous trial target contrast. **corresponds to p-values < .01.
Fig. S3. Serial dependence is modulated by relative target contrast. (a.) Left: Serial dependence curves and DoG fits to error data with high error trials omitted (i.e., on correct depth report trials following correct depth report trials), when no feedback was provided (green), when auditory feedback was provided (red), and when auditory + visual feedback was provided (blue), sorted according to the relative direction of the current trial's target with respect to the previous trial's target direction and split out by current trial target contrast. Shaded bands represent +/-1 SEM. **corresponds to bootstrapped p-values < .001; n.s. = non-significant; p-
Task feedback suggests a post-perceptual component to serial dependence

September 2023

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38 Reads

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5 Citations

Journal of Vision

Decisions across a range of perceptual tasks are biased toward past stimuli. Such serial dependence is thought to be an adaptive low-level mechanism that promotes perceptual stability across time. However, recent studies suggest post-perceptual mechanisms may also contribute to serially biased responses, calling into question a single locus of serial dependence and the nature of integration of past and present sensory inputs. We measured serial dependence in the context of a three-dimensional (3D) motion perception task where uncertainty in the sensory information varied substantially from trial to trial. We found that serial dependence varied with stimulus properties that impact sensory uncertainty on the current trial. Reduced stimulus contrast was associated with an increased bias toward the stimulus direction of the previous trial. Critically, performance feedback, which reduced sensory uncertainty, abolished serial dependence. These results provide clear evidence for a post-perceptual locus of serial dependence in 3D motion perception and support the role of serial dependence as a response strategy in the face of substantial sensory uncertainty.


Citations (52)


... In terms of network integration, numerous studies have reported changes in both stationary (Abboud & Cohen, 2019;Bauer et al., 2017;Burton et al., 2014;Hou et al., 2017;Hu et al., 2020;Huang et al., 2020;Liu et al., 2007;Striem-Amit et al., 2015;Wen et al., 2018) and dynamic FC (Pelland et al., 2017) following early sensory deprivation. Recently, we employed Hidden Markov Models (HMM) on resting-state fMRI (rs-fMRI) data from EBs, and showed that early visual deprivation alters FC temporal dynamics (Pedersini et al., 2024). Our findings revealed that EBs use to visit more than controls brain states that primarily activate unimodal regions, with heightened connectivity involving occipital areas, although the overall frequency of switching between brain states remains intact. ...

Reference:

Gray matter abnormalities in sight deprivation and sight restoration
Characterizing dynamic functional connectivity in congenitally blind people using Hidden Markov Models

... The association between bad quality of sleep and mood disturbances, with no influence of oxygen saturation, is consistent with the results of deterministic whole-brain tractography on diffusion magnetic resonance imaging (MRI) scans showing disruptions in the limbic system after COVID-19, particularly the uncinate fasciculus, the cingulum cingulate, the cingulum hippocampus, and the arcuate fasciculus, with no significant differences between hospitalized and non-hospitalized patients [51]. Four weeks after acute COVID-19, psychiatric symptoms were evident in 56% of 402 adults (300 hospitalized), with correlation between the scores on depression and anxiety with systemic inflammation and no correlation with oxygen saturation [52]. ...

Tracts in the limbic system show microstructural alterations post COVID-19 recovery
  • Citing Article
  • May 2024

Brain Communications

... More recently, motion-in-depth selectivity is further measured in area FST. By comparing motion-in-depth selectivity both in perspective cue and binocular cue (IOVD and CDOT cues) in areas MT and FST, Thompson et al. determined area FST represents motion-in-depth in a more cue-invariant manner compared to area MT [63]. This suggests a possible hierarchical representation for 3D motion within the dorsal visual pathway. ...

Hierarchical computation of 3D motion across macaque areas MT and FST

Cell Reports

... In addition, previous studies also debated a lot on the occurrence mechanisms underlying serial dependence. That is, whether serial dependence is purely perceptual or the post-perceptual abilities were involved in (e.g., Bliss & D'Esposito, [4]; Ceylan et al., [8,14,17,50]. Sun et al. [42,44] found the stimulus distribution affected the serial dependence in self-motion direction perception and argued that postperceptual abilities were involved in. ...

Task feedback suggests a post-perceptual component to serial dependence

Journal of Vision

... However, in this study, the clinical cohort was composed of individuals who received the eye surgery before the 2nd year from birth, thus before the closure of the sensitive period of visual development, raising an intriguing question: how does structural brain plasticity reverse after sight restoration received during adolescence? In a recent study, we found that sight recovery following eye surgery received during adolescence induced structural plasticity in late-visual white matter pathways (Pedersini et al., 2023), underscoring that white matter tracts are sensitive markers of structural brain plasticity following vision restoration. To further investigate anatomical changes following eye surgery, in this study we assessed gray matter alterations in the same clinical cohort of congenitally blind individuals who underwent eye surgery after the closure of the sensitive period of visual development. ...

White matter plasticity following cataract surgery in congenitally blind patients

Proceedings of the National Academy of Sciences

... It should be noted that these attentional inhomogeneities have typically been investigated using static stimuli, in effect focusing on cortical processing along the temporal pathway. This leaves open the possibility that attentional inhomogeneities are weak or absent for stimuli processed along the dorsal pathway, because the sensory inhomogeneities might be weak for such stimuli [17]. ...

Asymmetries in the discrimination of motion direction around the visual field

Journal of Vision

... Previous work established human homologs of MT and MST using 2D-motion localizers 19,20 . Both areas also show adaptation to 3D-motion stimuli 21 and direction of motion can be decoded from them as well as areas more anterior 22 . However, these studies primarily relied on stimuli that contained both 3D and 2D (retinal) motion signals. ...

Identifying cortical areas that underlie the transformation from 2D retinal to 3D head-centric motion signals

NeuroImage

... a) Noisy perception: Human perception of the world is inherently noisy and imperfect [10]. This noisiness can be due to several factors, such as individual differences in sensory acuity [11] and environmental conditions (e.g., poor lighting, weather). It has been argued that this visual limitation affected the pedestrian crossing decision [12]. ...

Humans make non-ideal inferences about world motion

Journal of Vision

... We use a minimal (i.e., as simple as possible) mathematical model to reproduce the experimental evidence gathered from a set of experiments. In this sense, our approach is closer to that used in dynamic cognitive sciences (see, e.g., [35]), and follows in the path of recent attempts to model human perception through Bayesian observers [36], [37], [38], [39]. Moreover, our model does not address the complex learning processes that lead to the formation of the above-mentioned mental model. ...

A General Framework for Inferring Bayesian Ideal Observer Models from Psychophysical Data

eNeuro

... The essence of spatial perception is depth perception, which refers in a general sense to the perception of spatial properties such as physical distance, size, and orientation, the perception of spatial relationships of surrounding objects, and the perception of the elements that comprise spatial relationships (Rosinol et al. 2021;Setiawan 2021), such as position, orientation, and distance as shown in Fig. 4c. Motion perception is the human eye's sense of the spatial displacement of things (Barton 2021;Thompson et al. 2021), as shown in Fig. 4d. ...

Perspective Cues Make Eye-specific Contributions to 3-D Motion Perception

Journal of Cognitive Neuroscience