Automatic volumetric segmentation of human visual retinotopic cortex

Linking Multi-Modal MRI to Clinical Measures of Visual Field Loss After Stroke

Loss of vision across large parts of the visual field is a common and devastating complication of cerebral strokes. In the clinic, this loss is quantified by measuring the sensitivity threshold across the field of vision using static perimetry. These methods rely on the ability of the patient to report the presence of lights in particular locations. While perimetry provides important information about the intactness of the visual field, the approach has some shortcomings. For example, it cannot distinguish where in the visual pathway the key processing deficit is located. In contrast, brain imaging can provide important information about anatomy, connectivity, and function of the visual pathway following stroke. In particular, functional magnetic resonance imaging (fMRI) and analysis of population receptive fields (pRF) can reveal mismatches between clinical perimetry and maps of cortical areas that still respond to visual stimuli after stroke. Here, we demonstrate how information from different brain imaging modalities-visual field maps derived from fMRI, lesion definitions from anatomical scans, and white matter tracts from diffusion weighted MRI data-provides a more complete picture of vision loss. For any given location in the visual field, the combination of anatomical and functional information can help identify whether vision loss is due to absence of gray matter tissue or likely due to white matter disconnection from other cortical areas. We present a combined imaging acquisition and visual stimulus protocol, together with a description of the analysis methodology, and apply it to datasets from four stroke survivors with homonymous field loss (two with hemianopia, two with quadrantanopia). For researchers trying to understand recovery of vision after stroke and clinicians seeking to stratify patients into different treatment pathways, this approach combines multiple, convergent sources of data to characterize the extent of the stroke damage. We show that such an approach gives a more comprehensive measure of residual visual capacity-in two particular respects: which locations in the visual field should be targeted and what kind of visual attributes are most suited for rehabilitation.

fMRI Retinotopic Mapping in Patients with Brain Tumors and Space-Occupying Brain Lesions in the Area of the Occipital Lobe

Simple Summary

Functional magnetic resonance imaging (fMRI) in patients with brain tumors enables the visualization of eloquent cortical areas and can be used for planning surgical interventions and assessing the risk of postoperative functional deficits. While preoperative fMRI paradigms used to determine the localization of speech-critical or motor areas dominate the literature, there are hardly any studies that investigate the retinotopic organization of the visual field in patients with occipital lesions or tumors. The aim of this study was to evaluate the effect of a brain tumor or space-occupying brain lesions on the retinotopic organization of the occipital cortex, the activation of and the functional connectivity between cortical areas involved in visual processing. We found a high degree of similarity in the activation profiles of patients and healthy controls, indicating that the retinotopic organization of the visual cortex can reliably be described by fMRI retinotopic mapping as part of the preoperative examination of patients with tumors and space-occupying brain lesions.

Abstract

Functional magnetic resonance imaging (fMRI) is a valuable tool in the clinical routine of neurosurgery when planning surgical interventions and assessing the risk of postoperative functional deficits. Here, we examined how the presence of a brain tumor or lesion in the area of the occipital lobe affects the results of fMRI retinotopic mapping. fMRI data were evaluated on a retrospectively selected sample of 12 patients with occipital brain tumors, 7 patients with brain lesions and 19 control subjects. Analyses of the cortical activation, percent signal change, cluster size of the activated voxels and functional connectivity were carried out using Statistical Parametric Mapping (SPM12) and the CONN and Marsbar toolboxes. We found similar but reduced patterns of cortical activation and functional connectivity between the two patient groups compared to a healthy control group. Here, we found that retinotopic organization was well-preserved in the patients and was comparable to that of the age-matched controls. The results also showed that, compared to the tumor patients, the lesion patients showed higher percent signal changes but lower values in the cluster sizes of the activated voxels in the calcarine fissure region. Our results suggest that the lesion patients exhibited results that were more similar to those of the control subjects in terms of the BOLD signal, whereas the extent of the activation was comparable to that of the tumor patients.

Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas

The visual cortex of the mouse brain can be divided into ten or more areas that each contain complete or partial retinotopic maps of the contralateral visual field. It is generally assumed that these areas represent discrete processing regions. In contrast to the conventional input-output characterizations of neuronal responses to standard visual stimuli, here we asked whether six of the core visual areas have responses that are functionally distinct from each other for a given visual stimulus set, by applying machine learning techniques to distinguish the areas based on their activity patterns. Visual areas defined by retinotopic mapping were examined using supervised classifiers applied to responses elicited by a range of stimuli. Using two distinct datasets obtained using wide-field and two-photon imaging, we show that the area labels predicted by the classifiers were highly consistent with the labels obtained using retinotopy. Furthermore, the classifiers were able to model the boundaries of visual areas using resting state cortical responses obtained without any overt stimulus, in both datasets. With the wide-field dataset, clustering neuronal responses using a constrained semi-supervised classifier showed graceful degradation of accuracy. The results suggest that responses from visual cortical areas can be classified effectively using data-driven models. These responses likely reflect unique circuits within each area that give rise to activity with stronger intra-areal than inter-areal correlations, and their responses to controlled visual stimuli across trials drive higher areal classification accuracy than resting state responses.

Grey-Matter Thickness of the Left But Not the Right Primary Visual Area Correlates with Autism Traits in Typically Developing Adults

We examined whether functional and structural variability in the primary visual area (V1) correlated with autism traits. Twenty-nine participants (16 males; M_Age = 26.4 years, SD_Age = 4.0 years) completed the autism-spectrum quotient (AQ) questionnaire prior to a magnetic resonance imaging session. The total AQ scores was used to assess the degree of self-reported autism traits. The average functional activation in V1 to visual stimulation and its average grey-matter thickness were calculated. There were no correlations between functional activation in V1 and autism traits. Conversely, grey-matter thickness of the left but not the right V1 correlated with autism traits. We conclude that structural changes in the left V1 could be a marker for the presence of autism traits.

High-density diffuse optical tomography for imaging human brain function

This review describes the unique opportunities and challenges for noninvasive optical mapping of human brain function. Diffuse optical methods offer safe, portable, and radiation free alternatives to traditional technologies like positron emission tomography or functional magnetic resonance imaging (fMRI). Recent developments in high-density diffuse optical tomography (HD-DOT) have demonstrated capabilities for mapping human cortical brain function over an extended field of view with image quality approaching that of fMRI. In this review, we cover fundamental principles of the diffusion of near infrared light in biological tissue. We discuss the challenges involved in the HD-DOT system design and implementation that must be overcome to acquire the signal-to-noise necessary to measure and locate brain function at the depth of the cortex. We discuss strategies for validation of the sensitivity, specificity, and reliability of HD-DOT acquired maps of cortical brain function. We then provide a brief overview of some clinical applications of HD-DOT. Though diffuse optical measurements of neurophysiology have existed for several decades, tremendous opportunity remains to advance optical imaging of brain function to address a crucial niche in basic and clinical neuroscience: that of bedside and minimally constrained high fidelity imaging of brain function.

Identification of the ventral occipital visual field maps in the human brain

The location and topography of the first three visual field maps in the human brain, V1-V3, are well agreed upon and routinely measured across most laboratories. The position of 4 ^th visual field map, ‘hV4’, is identified with less consistency in the neuroimaging literature.  Using magnetic resonance imaging data, we describe landmarks to help identify the position and borders of ‘hV4’. The data consist of anatomical images, visualized as cortical meshes to highlight the sulcal and gyral patterns, and functional data obtained from retinotopic mapping experiments, visualized as eccentricity and angle maps on the cortical surface.

Several features of the functional and anatomical data can be found across nearly all subjects and are helpful for identifying the location and extent of the hV4 map. The medial border of hV4 is shared with the posterior, ventral portion of V3, and is marked by a retinotopic representation of the upper vertical meridian. The anterior border of hV4 is shared with the VO-1 map, and falls on a retinotopic representation of the peripheral visual field, usually coincident with the posterior transverse collateral sulcus. The ventro-lateral edge of the map typically falls on the inferior occipital gyrus, where functional MRI artifacts often obscure the retinotopic data. Finally, we demonstrate the continuity of retinotopic parameters between hV4 and its neighbors; hV4 and V3v contain iso-eccentricity lines in register, whereas hV4 and VO-1 contain iso-polar angle lines in register.

Together, the multiple constraints allow for a consistent identification of the hV4 map across most human subjects.

Quantitative evaluation of fMRI retinotopic maps, from V1 to V4, for cognitive experiments

FMRI retinotopic mapping is a non-invasive technique for the delineation of low-level visual areas in individual subjects. It generally relies upon the analysis of functional responses to periodic visual stimuli that encode eccentricity or polar angle in the visual field. This technique is used in vision research when the precise assignation of brain activation to retinotopic areas is an issue. It involves processing steps computed with different algorithms and embedded in various software suites. Manual intervention may be needed for some steps. Although the diversity of the available processing suites and manual interventions may potentially introduce some differences in the final delineation of visual areas, no documented comparison between maps obtained with different procedures has been reported in the literature. To explore the effect of the processing steps on the quality of the maps obtained, we used two tools, BALC, which relies on a fully automated procedure, and BrainVoyager, where areas are delineated “by hand” on the brain surface. To focus on the mapping procedures specifically, we used the same SPM pipeline for pretreatment and the same tissue segmentation tool. We document the consistency and differences of the fMRI retinotopic maps obtained from “routine retinotopy” experiments on 10 subjects. The maps obtained by skilled users are never fully identical. However, the agreement between the maps, around 80% for low-level areas, is probably sufficient for most applications. Our results also indicate that assigning cognitive activations, following a specific experiment (here, color perception), to individual retinotopic maps is not free of errors. We provide measurements of this error, that may help for the cautious interpretation of cognitive activation projection onto fMRI retinotopic maps. On average, the magnitude of the error is about 20%, with much larger differences in a few subjects. More variability may even be expected with less trained users or using different acquisition parameters and preprocessing chains.

Functional and anatomical properties of human visual cortical fields

Human visual cortical fields (VCFs) vary in size and anatomical location across individual subjects. Here, we used functional magnetic resonance imaging (fMRI) with retinotopic stimulation to identify VCFs on the cortical surface. We found that aligning and averaging VCF activations across the two hemispheres provided clear delineation of multiple retinotopic fields in visual cortex. The results show that VCFs have consistent locations and extents in different subjects that provide stable and accurate landmarks for functional and anatomical mapping. Interhemispheric comparisons revealed minor differences in polar angle and eccentricity tuning in comparable VCFs in the left and right hemisphere, and somewhat greater intersubject variability in the right than left hemisphere. We then used the functional boundaries to characterize the anatomical properties of VCFs, including fractional anisotropy (FA), magnetization transfer ratio (MTR) and the ratio of T1W and T2W images and found significant anatomical differences between VCFs and between hemispheres.

Topography and areal organization of mouse visual cortex

To guide future experiments aimed at understanding the mouse visual system, it is essential that we have a solid handle on the global topography of visual cortical areas. Ideally, the method used to measure cortical topography is objective, robust, and simple enough to guide subsequent targeting of visual areas in each subject. We developed an automated method that uses retinotopic maps of mouse visual cortex obtained with intrinsic signal imaging (Schuett et al., 2002; Kalatsky and Stryker, 2003; Marshel et al., 2011) and applies an algorithm to automatically identify cortical regions that satisfy a set of quantifiable criteria for what constitutes a visual area. This approach facilitated detailed parcellation of mouse visual cortex, delineating nine known areas (primary visual cortex, lateromedial area, anterolateral area, rostrolateral area, anteromedial area, posteromedial area, laterointermediate area, posterior area, and postrhinal area), and revealing two additional areas that have not been previously described as visuotopically mapped in mice (laterolateral anterior area and medial area). Using the topographic maps and defined area boundaries from each animal, we characterized several features of map organization, including variability in area position, area size, visual field coverage, and cortical magnification. We demonstrate that higher areas in mice often have representations that are incomplete or biased toward particular regions of visual space, suggestive of specializations for processing specific types of information about the environment. This work provides a comprehensive description of mouse visuotopic organization and describes essential tools for accurate functional localization of visual areas.

Evaluating population receptive field estimation frameworks in terms of robustness and reproducibility

Within vision research retinotopic mapping and the more general receptive field estimation approach constitute not only an active field of research in itself but also underlie a plethora of interesting applications. This necessitates not only good estimation of population receptive fields (pRFs) but also that these receptive fields are consistent across time rather than dynamically changing. It is therefore of interest to maximize the accuracy with which population receptive fields can be estimated in a functional magnetic resonance imaging (fMRI) setting. This, in turn, requires an adequate estimation framework providing the data for population receptive field mapping. More specifically, adequate decisions with regard to stimulus choice and mode of presentation need to be made. Additionally, it needs to be evaluated whether the stimulation protocol should entail mean luminance periods and whether it is advantageous to average the blood oxygenation level dependent (BOLD) signal across stimulus cycles or not. By systematically studying the effects of these decisions on pRF estimates in an empirical as well as simulation setting we come to the conclusion that a bar stimulus presented at random positions and interspersed with mean luminance periods is generally most favorable. Finally, using this optimal estimation framework we furthermore tested the assumption of temporal consistency of population receptive fields. We show that the estimation of pRFs from two temporally separated sessions leads to highly similar pRF parameters.

Probabilistic Maps of Visual Topography in Human Cortex

The human visual system contains an array of topographically organized regions. Identifying these regions in individual subjects is a powerful approach to group-level statistical analysis, but this is not always feasible. We addressed this limitation by generating probabilistic maps of visual topographic areas in 2 standardized spaces suitable for use with adult human brains. Using standard fMRI paradigms, we identified 25 topographic maps in a large population of individual subjects (N = 53) and transformed them into either a surface- or volume-based standardized space. Here, we provide a quantitative characterization of the inter-subject variability within and across visual regions, including the likelihood that a given point would be classified as a part of any region (full probability map) and the most probable region for any given point (maximum probability map). By evaluating the topographic organization across the whole of visual cortex, we provide new information about the organization of individual visual field maps and large-scale biases in visual field coverage. Finally, we validate each atlas for use with independent subjects. Overall, the probabilistic atlases quantify the variability of topographic representations in human cortex and provide a useful reference for comparing data across studies that can be transformed into these standard spaces.

Reorganization of retinotopic maps after occipital lobe infarction

We studied patient JS, who had a right occipital infarct that encroached on visual areas V1, V2v, and VP. When tested psychophysically, he was very impaired at detecting the direction of motion in random dot displays where a variable proportion of dots moving in one direction (signal) were embedded in masking motion noise (noise dots). The impairment on this motion coherence task was especially marked when the display was presented to the upper left (affected) visual quadrant, contralateral to his lesion. However, with extensive training, by 11 months his threshold fell to the level of healthy participants. Training on the motion coherence task generalized to another motion task, the motion discontinuity task, on which he had to detect the presence of an edge that was defined by the difference in the direction of the coherently moving dots (signal) within the display. He was much better at this task at 8 than 3 months, and this improvement was associated with an increase in the activation of the human MT complex (hMT(+)) and in the kinetic occipital region as shown by repeated fMRI scans. We also used fMRI to perform retinotopic mapping at 3, 8, and 11 months after the infarct. We quantified the retinotopy and areal shifts by measuring the distances between the center of mass of functionally defined areas, computed in spherical surface-based coordinates. The functionally defined retinotopic areas V1, V2v, V2d, and VP were initially smaller in the lesioned right hemisphere, but they increased in size between 3 and 11 months. This change was not found in the normal, left hemisphere of the patient or in either hemispheres of the healthy control participants. We were interested in whether practice on the motion coherence task promoted the changes in the retinotopic maps. We compared the results for patient JS with those from another patient (PF) who had a comparable lesion but had not been given such practice. We found similar changes in the maps in the lesioned hemisphere of PF. However, PF was only scanned at 3 and 7 months, and the biggest shifts in patient JS were found between 8 and 11 months. Thus, it is important to carry out a prospective study with a trained and untrained group so as to determine whether the patterns of reorganization that we have observed can be further promoted by training.

Surface area of early visual cortex predicts individual speed of traveling waves during binocular rivalry

Binocular rivalry ensues when different images are presented to the 2 eyes with conscious perception alternating between the possible interpretations. For large rivalry displays, perceptual transitions are initiated at one location and spread to other parts of the visual field, a phenomenon termed "traveling wave." Previous studies investigated the underlying neural mechanisms of the traveling wave and surmised that primary visual cortex might play an important role. We used magnetic resonance imaging and behavioral measures in humans to explore how interindividual differences in observers' subjective experience of the wave are related to anatomical characteristics of cortical regions. We measured wave speed in participants and confirmed the long-term stability of the individual values. Retinotopic mapping was employed to delineate borders of visual areas V1-V3 in order to determine surface area and cortical thickness in those regions. Only the surface areas of V1 and V2, but not V3 showed a correlation with wave speed. For individuals with larger V1/V2 area, the traveling wave needed longer to spread across the same distance in visual space. Our results highlight the role of early visual areas in mediating binocular rivalry and suggest possible mechanisms for the correlation between surface area and the traveling waves.

Pattern-motion selective responses in MT, MST and the pulvinar of humans

Plaid stimuli are often used to investigate the mechanisms involved in the integration and segregation of motion information. Considering the perceptual importance of such mechanisms, only a very limited number of visual brain areas have been found to be specifically involved in motion integration. These are the human (h)MT+ complex, area V3 and the pulvinar. The hMT+ complex can be functionally subdivided into two separate areas, middle temporal area (MT) and medial superior temporal area (MST); however, it is currently unclear whether these distinct sub-regions have different responses to plaid stimuli. To address this issue we used functional magnetic resonance imaging to quantify the relative response of MT and MST to component and pattern motion. Participants viewed plaid stimuli that were constrained to result in the perception of either component motion (segregation of motion information) or pattern motion (integration of motion information). MT/MST segregation was achieved using a moving dot stimulus that allowed stimulation of each visual hemifield either in unison or separately. We found pattern motion selective responses in both MT and MST. Consistent with previous reports, activity indicative of pattern motion selectivity was also found in the pulvinar as well as in other extrastriate areas. These results demonstrate that MT, MST and the pulvinar are involved in the complex motion integration mechanisms that are triggered by plaid stimuli. This reinforces the concept that integrative computations take place in a distributed neuronal circuit both in cortical and sub-cortical networks.

Abnormal cortical processing of pattern motion in amblyopia: evidence from fMRI

Converging evidence from human psychophysics and animal neurophysiology indicates that amblyopia is associated with abnormal function of area MT, a motion sensitive region of the extrastriate visual cortex. In this context, the recent finding that amblyopic eyes mediate normal perception of dynamic plaid stimuli was surprising, as neural processing and perception of plaids has been closely linked to MT function. One intriguing potential explanation for this discrepancy is that the amblyopic eye recruits alternative visual brain areas to support plaid perception. This is the hypothesis that we tested. We used functional magnetic resonance imaging (fMRI) to measure the response of the amblyopic visual cortex and thalamus to incoherent and coherent motion of plaid stimuli that were perceived normally by the amblyopic eye. We found a different pattern of responses within the visual cortex when plaids were viewed by amblyopic as opposed to non-amblyopic eyes. The non-amblyopic eyes of amblyopes and control eyes differentially activated the hMT+ complex when viewing incoherent vs. coherent plaid motion, consistent with the notion that this region is centrally involved in plaid perception. However, for amblyopic eye viewing, hMT+ activation did not vary reliably with motion type. In a sub-set of our participants with amblyopia we were able to localize MT and MST within the larger hMT+ complex and found a lack of plaid motion selectivity in both sub-regions. The response of the pulvinar and ventral V3 to plaid stimuli also differed under amblyopic vs. non-amblyopic eye viewing conditions, however the response of these areas did vary according to motion type. These results indicate that while the perception of the plaid stimuli was constant for both amblyopic and non-amblyopic viewing, the network of neural areas that supported this perception was different.

The relationship between cortical magnification factor and population receptive field size in human visual cortex: constancies in cortical architecture

Receptive field (RF) sizes and cortical magnification factor (CMF) are fundamental organization properties of the visual cortex. At increasing visual eccentricity, RF sizes increase and CMF decreases. A relationship between RF size and CMF suggests constancies in cortical architecture, as their product, the cortical representation of an RF (point image), may be constant. Previous animal neurophysiology studies of this question yield conflicting results. Here, we use fMRI to determine the relationship between the population RF (pRF) and CMF in humans. In average and individual data, the product of CMF and pRF size, the population point image, is near constant, decreasing slightly with eccentricity in V1. Interhemisphere and subject variations in CMF, pRF size, and V1 surface area are correlated, and the population point image varies less than these properties. These results suggest a V1 cortical processing architecture of approximately constant size between humans. Up the visual hierarchy, to V2, V3, hV4, and LO1, the population point image decreases with eccentricity, and both the absolute values and rate of change increase. PRF sizes increase between visual areas and with eccentricity, but when expressed in V1 cortical surface area (i.e., corticocortical pRFs), they are constant across eccentricity in V2/V3. Thus, V2/V3, and to some degree hV4, sample from a constant extent of V1. This may explain population point image changes in later areas. Consequently, the constant factor determining pRF size may not be the relationship to the local CMF, but rather pRF sizes and CMFs in visual areas from which the pRF samples.

Imaging retinotopic maps in the human brain

A quarter-century ago visual neuroscientists had little information about the number and organization of retinotopic maps in human visual cortex. The advent of functional magnetic resonance imaging (MRI), a non-invasive, spatially-resolved technique for measuring brain activity, provided a wealth of data about human retinotopic maps. Just as there are differences amongst non-human primate maps, the human maps have their own unique properties. Many human maps can be measured reliably in individual subjects during experimental sessions lasting less than an hour. The efficiency of the measurements and the relatively large amplitude of functional MRI signals in visual cortex make it possible to develop quantitative models of functional responses within specific maps in individual subjects. During this last quarter-century, there has also been significant progress in measuring properties of the human brain at a range of length and time scales, including white matter pathways, macroscopic properties of gray and white matter, and cellular and molecular tissue properties. We hope the next 25years will see a great deal of work that aims to integrate these data by modeling the network of visual signals. We do not know what such theories will look like, but the characterization of human retinotopic maps from the last 25years is likely to be an important part of future ideas about visual computations.

Neuropsychological evidence for three distinct motion mechanisms

We describe psychophysical performance of two stroke patients with lesions in distinct cortical regions in the left hemisphere. Both patients were selectively impaired on direction discrimination in several local and global second-order but not first-order motion tasks. However, only patient FD was impaired on a specific bi-stable motion task where the direction of motion is biased by object similarity. We suggest that this bi-stable motion task may be mediated by a high-level attention or position based mechanism indicating a separate neurological substrate for a high-level attention or position-based mechanism. Therefore, these results provide evidence for the existence of at least three motion mechanisms in the human visual system: a low-level first- and second-order motion mechanism and a high-level attention or position-based mechanism.

A patient specific electro-mechanical model of the heart

This paper presents a patient specific deformable heart model that involves the known electrical and mechanical properties of the cardiac cells and tissue. The whole heart model comprises ten Tusscher's ventricular and Nygren's atrial cell models, the anatomical and electrophysiological model descriptions of the atria (introduced by Harrild et al.) and ventricle (given by Winslow et al.), and the mechanical model of the periodical cardiac contraction and resting phenomena proposed by Moireau et al. During the propagation of the depolarization wave, the kinetic, compositional and rotational anisotropy is handled by the tissue, organ and torso model. The applied patient specific parameters were determined by an evolutionary computation method. An intensive parameter reduction was performed using the abstract formulation of the searching space. This patient specific parameter representation enables the adjustment of deformable model parameters in real-time. The validation process was performed using simultaneously measured ECG and ultrasound image records that were compared with simulated signals and shapes using an abstract, parameterized evaluation criterion.

The contrast dependence of the cortical fMRI deficit in amblyopia; a selective loss at higher contrasts

Although there is general agreement that the fMRI cortical response is reduced in humans with amblyopia, the deficit is subtle and has little correlation with threshold-based psychophysics. From a purely contrast sensitivity perspective, one would expect fMRI responses to be selectively reduced for stimuli of low contrasts. However, to date, all fMRI stimuli used in studies of amblyopia have been of high contrast. Furthermore, if the deficit is selective for low contrasts, one would expect it to reflect a selective M-cell loss, because M-cells have much higher contrast gain than P-cells and make a larger contribution to the threshold detection of stimuli of low spatial and medium temporal frequencies. To test these two predictions, we compared % BOLD response between the eyes of normals and amblyopes for low- and high-contrast stimuli using a phase-encoded design. The results suggest that the fMRI deficit in amblyopia depends upon stimulus contrast and that it is greater at high contrasts. This is consistent with a selective P-cell contrast deficit at a precortical or early cortical site.

The amblyopic deficit and its relationship to geniculo-cortical processing streams

Amblyopia or lazy eye is the most common cause of uniocular blindness in adults and is caused by a disruption to normal visual development as a consequence of unmatched inputs from the two eyes in early life, arising from a turned eye (strabismus), unequal refractive error (anisometropia), or form deprivation (e.g., cataract). Using high-field functional magnetic resonance imaging in a group of human adults with amblyopia, we previously demonstrated that reduced responses are observable at a thalamic level, that of the lateral geniculate nucleus (LGN). Here we investigate the selectivity of this deficit by using chromatic and achromatic stimuli that are designed to bias stimulation to one or other of the three ascending pathways (the parvocellular, magnocellular, and koniocellular). We find the greatest LGN deficit is for stimuli modulated along the chromatic, L/M cone opponent axis of color space, suggesting a selective loss of parvocellular function in the LGN. We also demonstrate a cortical deficit that involves all the visual areas studied (V1, V2, V3, VP, V3A, V4), and we find this is greatest for the two chromatic responses (S cone opponent and L/M cone opponent) versus the achromatic response, as might be expected from a loss of segregation of chromatic pathways in the cortex.

Selectivity as well as sensitivity loss characterizes the cortical spatial frequency deficit in amblyopia

The processing deficit in amblyopia is not restricted to just high spatial frequencies but also involves low-medium spatial frequency processing, for suprathreshold stimuli with a broad orientational bandwidth. This is the case in all three forms of amblyopia; strabismic, anisometropic, and deprivation. Here we use both a random block design and a phase-encoded design to ascertain (1) the extent to which fMRI activation is reduced at low-mid spatial frequencies in different visual areas, (2) how accurately spatial frequency is mapped across the amblyopic cortex. We report a loss of function to suprathreshold low-medium spatial frequency stimuli that involves more than just area V1, suggesting a diffuse loss in spatial frequency processing in a number of different cortical areas. An analysis of the fidelity of the spatial frequency cortical map reveals that many voxels lose their spatial frequency preference when driven by the amblyopic eye, suggesting a broader tuning for spatial frequency for neurons driven by the amblyopic eye within this low-mid spatial frequency range.

The emerging discipline of Computational Functional Anatomy

Computational Functional Anatomy (CFA) is the study of functional and physiological response variables in anatomical coordinates. For this we focus on two things: (i) the construction of bijections (via diffeomorphisms) between the coordinatized manifolds of human anatomy, and (ii) the transfer (group action and parallel transport) of functional information into anatomical atlases via these bijections. We review advances in the unification of the bijective comparison of anatomical submanifolds via point-sets including points, curves and surface triangulations as well as dense imagery. We examine the transfer via these bijections of functional response variables into anatomical coordinates via group action on scalars and matrices in DTI as well as parallel transport of metric information across multiple templates which preserves the inner product.

Color responses of the human lateral geniculate nucleus: [corrected] selective amplification of S-cone signals between the lateral geniculate nucleno and primary visual cortex measured with high-field fMRI

The lateral geniculate nucleus (LGN) is the primary thalamic nucleus that relays visual information from the retina to the primary visual cortex (V1) and has been extensively studied in non-human primates. A key feature of the LGN is the segregation of retinal inputs into different cellular layers characterized by their differential responses to red-green (RG) color (L/M opponent), blue-yellow (BY) color (S-cone opponent) and achromatic (Ach) contrast. In this study we use high-field functional magnetic resonance imaging (4 tesla, 3.6 × 3.6 × 3 mm³) to record simultaneously the responses of the human LGN and V1 to chromatic and Ach contrast to investigate the LGN responses to color, and how these are modified as information transfers between LGN and cortex. We find that the LGN has a robust response to RG color contrast, equal to or greater than the Ach response, but a significantly poorer sensitivity to BY contrast. In V1 at low temporal rates (2 Hz), however, the sensitivity of the BY color pathway is selectively enhanced, rising in relation to the RG and Ach responses. We find that this effect generalizes across different stimulus contrasts and spatial stimuli (1-d and 2-d patterns), but is selective for temporal frequency, as it is not found for stimuli at 8 Hz. While the mechanism of this cortical enhancement of BY color vision and its dynamic component is unknown, its role may be to compensate for a weak BY signal originating from the sparse distribution of neurons in the retina and LGN.

Sparsely distributed contours dominate extra-striate responses to complex scenes

The human visual system exploits redundancy in natural scenes to derive useful information. Such redundancy is frequently associated with either contours or textures within images. In this study we use fMRI to evaluate how the total amount of contrast-energy contained in contours and textures within natural images affect responses in visual cortex. We used both the entire natural image and parts of it containing predominantly contour or texture information. We modified these natural images in order to match other image properties that are known to affect cortical responses as closely as possible. These modified natural images, i.e. pseudo-natural images, remain highly recognizable. We also used synthetic images without recognizable content but with closely matched image properties. We report that most of the primary visual cortex (V1) signal variations are explained by the total amount of contrast-energy in the images. Extra-striate visual cortex, on the other hand, is driven strongest by images containing sparsely distributed contours; independent of contrast-energy amount or recognizable image content. These results provide evidence for an initial representation of natural images in V1 based on local oriented filters. Later visual cortex (and to a modest degree V1) incorporates a facilitation of contour-based structure and suppressive interactions that effectively amplify sparse-contour information within natural images.

Functional organization of human visual cortex in occipital polymicrogyria

Polymicrogyrias (PMG) are cortical malformations resulting from developmental abnormalities. In animal models PMG has been associated with abnormal anatomy, function, and organization. The purpose of this study was to describe the function and organization of human polymicrogyric cortex using functional magnetic resonance imaging. Three patients with epilepsy and bilateral parasagittal occipital polymicrogyri were studied. They all had normal vision as tested by Humphrey visual field perimetry. The functional organization of the visual cortex was reconstructed using phase-encoded retinotopic mapping analysis. This method sequentially stimulates each point in the visual field along the axes of a polar-coordinate system, thereby reconstructing the representation of the visual field on the cortex. We found normal cortical responses and organization of early visual areas (V1, V2, and V3/VP). The locations of these visual areas overlapped substantially with the PMG. In five out of six hemispheres the reconstructed primary visual cortex completely fell within polymicrogyric areas. Our results suggest that human polymicrogyric cortex is not only organized in a normal fashion, but is also actively involved in processing of visual information and contributes to normal visual perception.

Visual field maps in human cortex

Much of the visual cortex is organized into visual field maps: nearby neurons have receptive fields at nearby locations in the image. Mammalian species generally have multiple visual field maps with each species having similar, but not identical, maps. The introduction of functional magnetic resonance imaging made it possible to identify visual field maps in human cortex, including several near (1) medial occipital (V1,V2,V3), (2) lateral occipital (LO-1,LO-2, hMT+), (3) ventral occipital (hV4, VO-1, VO-2), (4) dorsal occipital (V3A, V3B), and (5) posterior parietal cortex (IPS-0 to IPS-4). Evidence is accumulating for additional maps, including some in the frontal lobe. Cortical maps are arranged into clusters in which several maps have parallel eccentricity representations, while the angular representations within a cluster alternate in visual field sign. Visual field maps have been linked to functional and perceptual properties of the visual system at various spatial scales, ranging from the level of individual maps to map clusters to dorsal-ventral streams. We survey recent measurements of human visual field maps, describe hypotheses about the function and relationships between maps, and consider methods to improve map measurements and characterize the response properties of neurons comprising these maps.

Population receptive field estimates in human visual cortex

We introduce functional MRI methods for estimating the neuronal population receptive field (pRF). These methods build on conventional visual field mapping that measures responses to ring and wedge patterns shown at a series of visual field locations and estimates the single position in the visual field that produces the largest response. The new method computes a model of the population receptive field from responses to a wide range of stimuli and estimates the visual field map as well as other neuronal population properties, such as receptive field size and laterality. The visual field maps obtained with the pRF method are more accurate than those obtained using conventional visual field mapping, and we trace with high precision the visual field maps to the center of the foveal representation. We report quantitative estimates of pRF size in medial, lateral and ventral occipital regions of human visual cortex. Also, we quantify the amount of input from ipsi- and contralateral visual fields. The human pRF size estimates in V1-V3 agree well with electrophysiological receptive field measurements at a range of eccentricities in corresponding locations within monkey and human visual field maps. The pRF method is non-invasive and can be applied to a wide range of conditions when it is useful to link fMRI signals in the visual pathways to neuronal receptive fields.

Cortical specialization for concentric shape processing

It is current dogma that neurons in primary visual cortex extract local edges from the scene, from which later visual areas reconstruct more meaningful shapes. In intermediate areas, such as area V4, responses are driven by features more complex than local oriented edges but more basic than meaningful shapes. The present study was motivated by the proposal that concentric (circular) shape processing is an important aspect of intermediate shape processing and is proposed to occur in area V4. However, previous studies are not able to discriminate between the number of orientations within the image nor how these orientations vary across space (orientation gradient, contrast or curvature) as opposed to concentric shape processing per se. We address the question whether V4 responses are driven by curvature or circularity. We use fMRI and tightly controlled narrowband stimuli with identical local and global properties. These patterns either form random or circular patterns with tightly matched orientation gradients and therefore similar curvature. We find stronger responses to circular patterns in areas V3/VP and V4. Our results suggest that extracting circular shape is an important step in intermediate shape processing.

The fidelity of the cortical retinotopic map in human amblyopia

To delineate the fidelity of the functional cortical organization in humans with amblyopia, we undertook an investigation into how spatial information is mapped across the visual cortex in amblyopic observers. We assessed whether the boundaries of the visual areas controlled by the amblyopic and fellow fixing eye are in the same position, the fidelity of the retinotopic map within different cortical areas and the average receptive field size in different visual areas. The functional organization of the visual cortex was reconstructed using a fMRI phase-encoded retinotopic mapping analysis. This method sequentially stimulates each point in the visual field along the axes of a polar-coordinate system, thereby reconstructing the representation of the visual field on the cortex. We found that the cortical areas were very similar in normals and amblyopes, with only small differences in boundary positions of different visual areas between fixing and fellow amblyopic eye activation. Within these corresponding visual areas, we did find anomalies in retinotopy in some but not all amblyopes that were not simply a consequence of the poorer functional responses and affected central and peripheral field regions. Only a small increase in the average (or collective) receptive field size was found for full-field representation in amblyopes and none at all for central field representation. The former may simply be a consequence of the poorer functional responses.

Selectivity of human retinotopic visual cortex to S-cone-opponent, L/M-cone-opponent and achromatic stimulation

Our aim was to make a quantitative comparison of the response of the different visual cortical areas to selective stimulation of the two different cone-opponent pathways [long- and medium-wavelength (L/M)- and short-wavelength (S)-cone-opponent] and the achromatic pathway under equivalent conditions. The appropriate stimulus-contrast metric for the comparison of colour and achromatic sensitivity is unknown, however, and so a secondary aim was to investigate whether equivalent fMRI responses of each cortical area are predicted by stimulus contrast matched in multiples of detection threshold that approximately equates for visibility, or direct (cone) contrast matches in which psychophysical sensitivity is uncorrected. We found that the fMRI response across the two colour and achromatic pathways is not well predicted by threshold-scaled stimuli (perceptual visibility) but is better predicted by cone contrast, particularly for area V1. Our results show that the early visual areas (V1, V2, V3, VP and hV4) all have robust responses to colour. No area showed an overall colour preference, however, until anterior to V4 where we found a ventral occipital region that has a significant preference for chromatic stimuli, indicating a functional distinction from earlier areas. We found that all of these areas have a surprisingly strong response to S-cone stimuli, at least as great as the L/M response, suggesting a relative enhancement of the S-cone cortical signal. We also identified two areas (V3A and hMT+) with a significant preference for achromatic over chromatic stimuli, indicating a functional grouping into a dorsal pathway with a strong magnocellular input.

Modulation of V1 Activity by Shape: Image-Statistics or Shape-Based Perception?

It is current dogma that neurons in primary visual cortex extract local edges from the scene from which later visual areas reconstruct more meaningful shapes. Recent neuroimaging studies, however, have shown V1 modulations by the degree of structure in the image (shape). These V1 modulations due to the level of shape coherence have been explained in one of two possible ways: due to changes in image statistics or shape-based perceptual influences from higher visual areas. Here we compare both hypotheses using stimuli composed of Gabor arrays constructed to form circular shapes that can be successively degraded by manipulating the orientations of individual Gabors while maintaining local and global statistics. In a first experiment, we confirm that V1 responses are inversely correlated with the degree of structure in the image. In a second experiment, stimulus predictions are compared based on the degree of circular shape or change in the image statistic varied (orientation variance) in the image. We find that these V1 modulations to shape change are correlated with low-level changes in orientation contrast rather than shape perception per se.

Multifocal fMRI mapping of visual cortical areas

The multifocal mapping of electroretinograms and visual evoked potentials has established an important role in both basic research and in diagnostic procedures. We have developed a multifocal mapping method for fMRI, which allows detailed analysis of multiple local visual field representations in the cortex with excellent spatial resolution. Visual field was divided into 60 regions in a dartboard configuration, scaled according to the human magnification factor. Within blocks of 7 s, half of the regions were stimulated with checkerboard patterns contrast reversing at 8 reversals per second, while the other half remained inactive at uniform luminance. The subset of active regions changed with each 7-s block, according to an orthogonal design. Functional MRI was done with a 3-T GE Signa and analyzed with SPM2. A general linear model was fitted producing activation maps for each of the 60 regions, and local signal changes were quantified from V1. These activation maps were next assigned to 3D surface models of the cortical sheet, and then unfolded, using the Brain à la Carte software package. Phase-encoded retinotopic analysis of conventional design served as qualitative comparison data. With multifocal fMRI, all regions were mapped with good signal-to-noise ratio in V1, and subsets of regions showed activation in V2 and V3. This method allows rapid and direct exploration of multiple local visual responses, and is thus able to give complementary information to phase encoded mapping of retinotopic areas.

Linking retinotopic fMRI mapping and anatomical probability maps of human occipital areas V1 and V2

Using functional MRI, we characterized field sign maps of the occipital cortex and created three-dimensional maps of these areas. By averaging the individual maps into group maps, probability maps of functionally defined V1 or V2 were determined and compared to anatomical probability maps of Brodmann areas BA17 and BA18 derived from cytoarchitectonic analysis (Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., Zilles, K., 2000. Brodmann's areas 17 and 18 brought into stereotaxic space-where and how variable? NeuroImage 11, 66-84). Comparison of areas BA17/V1 and BA18/V2 revealed good agreement of the anatomical and functional probability maps. Taking into account that our functional stimulation (due to constraints of the visual angle of stimulation achievable in the MR scanner) only identified parts of V1 and V2, for statistical evaluation of the spatial correlation of V1 and BA17, or V2 and BA18, respectively, the a priori measure kappa was calculated testing the hypothesis that a region can only be part of functionally defined V1 or V2 if it is also in anatomically defined BA17 or BA18, respectively. kappa = 1 means the hypothesis is fully true, kappa = 0 means functionally and anatomically defined visual areas are independent. When applying this measure to the probability maps, kappa was equal to 0.84 for both V1/BA17 and V2/BA18. The data thus show a good correspondence of functionally and anatomically derived segregations of early visual processing areas and serve as a basis for employing anatomical probability maps of V1 and V2 in group analyses to characterize functional activations of early visual processing areas.

Identification of the neural sources of the pattern-reversal VEP

This study aimed to characterize the neural generators of the early components of the visual-evoked potential (VEP) to pattern-reversal gratings. Multichannel scalp recordings of VEPs and dipole modeling techniques were combined with functional magnetic resonance imaging (fMRI) and retinotopic mapping in order to estimate the locations of the cortical sources giving rise to VEP components in the first 200 ms poststimulus. Dipole locations were seeded to visual cortical areas in which fMRI activations were elicited by the same stimuli. The results provide strong evidence that the first major component of the VEP elicited by a pattern-reversal stimulus (N75/P85) arises from surface-negative activity in the primary visual cortex (area V1). Subsequent waveform components could be accounted for by dipoles that were in close proximity to fMRI activations in the following cortical areas: P95 (area MT/V5), P125/N135 (area V1), N150 (transverse parietal sulcus, TPS), N160 (ventral occipital areas VP, V4v, and V4/V8), and N180 (dorsal occipital areas V3A/V7). These results provide a detailed spatiotemporal profile of the cortical origins of the pattern-reversal VEP, which should enhance its utility in both clinical and basic studies of visual-perceptual processing.

Computational anatomy: shape, growth, and atrophy comparison via diffeomorphisms

Computational anatomy (CA) is the mathematical study of anatomy I in I = I(alpha) o G, an orbit under groups of diffeomorphisms (i.e., smooth invertible mappings) g in G of anatomical exemplars I(alpha) in I. The observable images are the output of medical imaging devices. There are three components that CA examines: (i) constructions of the anatomical submanifolds, (ii) comparison of the anatomical manifolds via estimation of the underlying diffeomorphisms g in G defining the shape or geometry of the anatomical manifolds, and (iii) generation of probability laws of anatomical variation P(.) on the images I for inference and disease testing within anatomical models. This paper reviews recent advances in these three areas applied to shape, growth, and atrophy.