Characterisation of laminar and vascular spatiotemporal dynamics of CBV and BOLD signals using VASO and ME-GRE at 7T in humans

Interpretation of cortical laminar functional magnetic resonance imaging (fMRI) activity requires detailed knowledge of the spatiotemporal haemodynamic response across vascular compartments due to the well-known vascular biases (e.g. the draining veins). Further complications arise from the spatiotemporal hemodynamic response that differs depending on the duration of stimulation. This information is crucial for future studies using depth-dependent cerebral blood volume (CBV) measurements, which promise higher specificity for the cortical microvasculature than the blood oxygenation level dependent (BOLD) contrast. To date, direct information about CBV dynamics with respect to stimulus duration, cortical depth and vasculature is missing in humans. Therefore, we characterized the cortical depth-dependent CBV-haemodynamic responses across a wide set of stimulus durations with 0.9 mm isotropic spatial and 0.785 seconds effective temporal resolution in humans using slice-selective slab-inversion vascular space occupancy (SS-SI VASO). Additionally, we investigated signal contributions from macrovascular compartments using fine-scale vascular information from multi-echo gradient-echo (ME-GRE) data at 0.35 mm isotropic resolution. In total, this resulted in >7.5h of scanning per participant (n=5). We have three major findings: (I) While we could demonstrate that 1 second stimulation is viable using VASO, more than 12 seconds stimulation provides better CBV responses in terms of specificity to microvasculature, but durations beyond 24 seconds of stimulation may be wasteful for certain applications. (II) We observe that CBV responses show dilation patterns across the cortex. (III) While we found increasingly strong BOLD signal responses in vessel-dominated voxels with longer stimulation durations, we found increasingly strong CBV signal responses in vessel-dominated voxels only until 4 second stimulation durations. After 4 seconds, only the signal from non-vessel dominated voxels kept increasing. This might explain why CBV responses are more specific to the underlying neuronal activity for long stimulus durations.

Layer-fMRI VASO with short stimuli and event-related designs at 7 T

Layers and columns are the dominant processing units in the human (neo)cortex at the mesoscopic scale. While the blood oxygenation dependent (BOLD) signal has a high detection sensitivity, it is biased towards unwanted signals from large draining veins at the cortical surface. The additional fMRI contrast of vascular space occupancy (VASO) has the potential to augment the neuroscientific interpretability of layer-fMRI results by means of capturing complementary information of locally specific changes in cerebral blood volume (CBV). Specifically, VASO is not subject to unwanted sensitivity amplifications of large draining veins. Because of constrained sampling efficiency, it has been mainly applied in combination with efficient block task designs and long trial durations. However, to study cognitive processes in neuroscientific contexts, or probe vascular reactivity, short stimulation periods are often necessary. Here, we developed a VASO acquisition procedure with a short acquisition period and sub-millimeter resolution. During visual event-related stimulation, we show reliable responses in visual cortices within a reasonable number of trials (∼20). Furthermore, the short TR and high spatial specificity of our VASO implementation enabled us to show differences in laminar reactivity and onset times. Finally, we explore the generalizability to a different stimulus modality (somatosensation). With this, we showed that CBV-sensitive VASO provides the means to capture layer-specific haemodynamic responses with high spatio-temporal resolution and is able to be used with event-related paradigms.

Imaging the columnar functional organization of human area MT+ to axis-of-motion stimuli using VASO at 7 Tesla

Cortical columns of direction-selective neurons in the motion sensitive area (MT) have been successfully established as a microscopic feature of the neocortex in animals. The same property has been investigated at mesoscale (<1 mm) in the homologous brain area (hMT+, V5) in living humans by using ultra-high field functional magnetic resonance imaging (fMRI). Despite the reproducibility of the selective response to axis-of-motion stimuli, clear quantitative evidence for the columnar organization of hMT+ is still lacking. Using cerebral blood volume (CBV)-sensitive fMRI at 7 Tesla with submillimeter resolution and high spatial specificity to microvasculature, we investigate the columnar functional organization of hMT+ in 5 participants perceiving axis-of-motion stimuli for both blood oxygenation level dependent (BOLD) and vascular space occupancy (VASO) contrast mechanisms provided by the used slice-selective slab-inversion (SS-SI)-VASO sequence. With the development of a new searchlight algorithm for column detection, we provide the first quantitative columnarity map that characterizes the entire 3D hMT+ volume. Using voxel-wise measures of sensitivity and specificity, we demonstrate the advantage of using CBV-sensitive fMRI to detect mesoscopic cortical features by revealing higher specificity of axis-of-motion cortical columns for VASO as compared to BOLD contrast. These voxel-wise metrics also provide further insights on how to mitigate the highly debated draining veins effect. We conclude that using CBV-VASO fMRI together with voxel-wise measurements of sensitivity, specificity and columnarity offers a promising avenue to quantify the mesoscopic organization of hMT+ with respect to axis-of-motion stimuli. Furthermore, our approach and methodological developments are generalizable and applicable to other human brain areas where similar mesoscopic research questions are addressed.

Laminar VASO fMRI in focal hand dystonia patients

Focal Hand Dystonia (FHD) is a disabling movement disorder characterized by involuntary movements, cramps and spasms. It is associated with pathological neural microcircuits in the cortical somatosensory system. While invasive preclinical modalities allow researchers to probe specific neural microcircuits of cortical layers and columns, conventional functional magnetic resonance imaging (fMRI) cannot resolve such small neural computational units. In this study, we take advantage of recent developments in ultra-high-field MRI hardware and MR-sequences to capture altered digit representations and laminar processing in FHD patients. We aim to characterize the capability and challenges of layer-specific imaging and analysis tools in resolving laminar and columnar structures in clinical research setups. We scanned N = 4 affected and N = 5 unaffected hemispheres at 7T and found consistent results of altered neural microcircuitry in FHD patients: 1) In affected hemispheres of FHD patients, we found a breakdown of ordered finger representation in the primary somatosensory cortex, as suggested from previous low-resolution fMRI. 2) In affected primary motor cortices of FHD patients, we furthermore found increased fMRI activity in superficial cortico-cortical neural input layers (II/III), compared to relatively weaker activity in the cortico-spinal output layers (Vb/VI). Overall, we show that layer-fMRI acquisition and analysis tools have the potential to address clinically-driven neuroscience research questions about altered computational mechanisms at the spatial scales that were previously only accessible in animal models. We believe that this study paves the way for easier translation of preclinical work into clinical research in focal hand dystonia and beyond.

Selective attention sharpens population receptive fields in human auditory cortex

Selective attention enables the preferential processing of relevant stimulus aspects. Invasive animal studies have shown that attending a sound feature rapidly modifies neuronal tuning throughout the auditory cortex. Human neuroimaging studies have reported enhanced auditory cortical responses with selective attention. To date, it remains unclear how the results obtained with functional magnetic resonance imaging (fMRI) in humans relate to the electrophysiological findings in animal models. Here we aim to narrow the gap between animal and human research by combining a selective attention task similar in design to those used in animal electrophysiology with high spatial resolution ultra-high field fMRI at 7 Tesla. Specifically, human participants perform a detection task, whereas the probability of target occurrence varies with sound frequency. Contrary to previous fMRI studies, we show that selective attention resulted in population receptive field sharpening, and consequently reduced responses, at the attended sound frequencies. The difference between our results to those of previous fMRI studies supports the notion that the influence of selective attention on auditory cortex is diverse and may depend on context, stimulus, and task.

Non-Neural Factors Influencing BOLD Response Magnitudes within Individual Subjects

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

Using high spatial resolution fMRI to understand representation in the auditory network

Following rapid methodological advances, ultra-high field (UHF) functional and anatomical magnetic resonance imaging (MRI) has been repeatedly and successfully used for the investigation of the human auditory system in recent years. Here, we review this work and argue that UHF MRI is uniquely suited to shed light on how sounds are represented throughout the network of auditory brain regions. That is, the provided gain in spatial resolution at UHF can be used to study the functional role of the small subcortical auditory processing stages and details of cortical processing. Further, by combining high spatial resolution with the versatility of MRI contrasts, UHF MRI has the potential to localize the primary auditory cortex in individual hemispheres. This is a prerequisite to study how sound representation in higher-level auditory cortex evolves from that in early (primary) auditory cortex. Finally, the access to independent signals across auditory cortical depths, as afforded by UHF, may reveal the computations that underlie the emergence of an abstract, categorical sound representation based on low-level acoustic feature processing. Efforts on these research topics are underway. Here we discuss promises as well as challenges that come with studying these research questions using UHF MRI, and provide a future outlook.

LayNii: A software suite for layer-fMRI

High-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed opensource and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain 'layerification' and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.

Improving a probabilistic cytoarchitectonic atlas of auditory cortex using a novel method for inter-individual alignment

The human superior temporal plane, the site of the auditory cortex, displays high inter-individual macro-anatomical variation. This questions the validity of curvature-based alignment (CBA) methods for in vivo imaging data. Here, we have addressed this issue by developing CBA+, which is a cortical surface registration method that uses prior macro-anatomical knowledge. We validate this method by using cytoarchitectonic areas on 10 individual brains (which we make publicly available). Compared to volumetric and standard surface registration, CBA+ results in a more accurate cytoarchitectonic auditory atlas. The improved correspondence of micro-anatomy following the improved alignment of macro-anatomy validates the superiority of CBA+ compared to CBA. In addition, we use CBA+ to align in vivo and postmortem data. This allows projection of functional and anatomical information collected in vivo onto the cytoarchitectonic areas, which has the potential to contribute to the ongoing debate on the parcellation of the human auditory cortex.

Feedback contribution to surface motion perception in the human early visual cortex

Human visual surface perception has neural correlates in early visual cortex, but the role of feedback during surface segmentation in human early visual cortex remains unknown. Feedback projections preferentially enter superficial and deep anatomical layers, which provides a hypothesis for the cortical depth distribution of fMRI activity related to feedback. Using ultra-high field fMRI, we report a depth distribution of activation in line with feedback during the (illusory) perception of surface motion. Our results fit with a signal re-entering in superficial depths of V1, followed by a feedforward sweep of the re-entered information through V2 and V3. The magnitude and sign of the BOLD response strongly depended on the presence of texture in the background, and was additionally modulated by the presence of illusory motion perception compatible with feedback. In summary, the present study demonstrates the potential of depth-resolved fMRI in tackling biomechanical questions on perception.

A 7 Tesla fMRI investigation of human tinnitus percept in cortical and subcortical auditory areas

Tinnitus is a clinical condition defined by hearing a sound in the absence of an objective source. Early experiments in animal models have suggested that tinnitus stems from an alteration of processing in the auditory system. However, translating these results to humans has proven challenging. One limiting factor has been the insufficient spatial resolution of non-invasive measurement techniques to investigate responses in subcortical auditory nuclei, like the inferior colliculus and the medial geniculate body (MGB). Here we employed ultra-high field functional magnetic resonance imaging (UHF-fMRI) at 7 Tesla to investigate the frequency-specific processing in sub-cortical and cortical regions in a cohort of six tinnitus patients and six hearing loss matched controls. We used task-based fMRI to perform tonotopic mapping and compared the magnitude and tuning of frequency-specific responses between the two groups. Additionally, we used resting-state fMRI to investigate the functional connectivity. Our results indicate frequency-unspecific reductions in the selectivity of frequency tuning that start at the level of the MGB and continue in the auditory cortex, as well as reduced thalamocortical and cortico-cortical connectivity with tinnitus. These findings suggest that tinnitus may be associated with reduced inhibition in the auditory pathway, potentially leading to increased neural noise and reduced functional connectivity. Moreover, these results indicate the relevance of high spatial resolution UHF-fMRI for the investigation of the role of sub-cortical auditory regions in tinnitus.

Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T

Studying the human subcortical auditory system non-invasively is challenging due to its small, densely packed structures deep within the brain. Additionally, the elaborate three-dimensional (3-D) structure of the system can be difficult to understand based on currently available 2-D schematics and animal models. Wfe addressed these issues using a combination of histological data, post mortem magnetic resonance imaging (MRI), and in vivo MRI at 7 Tesla. We created anatomical atlases based on state-of-the-art human histology (BigBrain) and postmortem MRI (50 µm). We measured functional MRI (fMRI) responses to natural sounds and demonstrate that the functional localization of subcortical structures is reliable within individual participants who were scanned in two different experiments. Further, a group functional atlas derived from the functional data locates these structures with a median distance below 2 mm. Using diffusion MRI tractography, we revealed structural connectivity maps of the human subcortical auditory pathway both in vivo (1050 µm isotropic resolution) and post mortem (200 µm isotropic resolution). This work captures current MRI capabilities for investigating the human subcortical auditory system, describes challenges that remain, and contributes novel, openly available data, atlases, and tools for researching the human auditory system.

The Relation between Color Spaces and Compositional Data Analysis Demonstrated with Magnetic Resonance Image Processing Applications

This paper presents a novel application of compositional data analysis methods in the context of color image processing. A vector decomposition method is proposed to reveal compositional components of any vector with positive components followed by compositional data analysis to demonstrate the relation between color space concepts such as hue and saturation to their compositional counterparts. The proposed methods are applied to a magnetic resonance imaging dataset acquired from a living human brain and a digital color photograph to perform image fusion. Potential future applications in magnetic resonance imaging are mentioned and the benefits/disadvantages of the proposed methods are discussed in terms of color image processing.

A scalable method to improve gray matter segmentation at ultra high field MRI

High-resolution (functional) magnetic resonance imaging (MRI) at ultra high magnetic fields (7 Tesla and above) enables researchers to study how anatomical and functional properties change within the cortical ribbon, along surfaces and across cortical depths. These studies require an accurate delineation of the gray matter ribbon, which often suffers from inclusion of blood vessels, dura mater and other non-brain tissue. Residual segmentation errors are commonly corrected by browsing the data slice-by-slice and manually changing labels. This task becomes increasingly laborious and prone to error at higher resolutions since both work and error scale with the number of voxels. Here we show that many mislabeled, non-brain voxels can be corrected more efficiently and semi-automatically by representing three-dimensional anatomical images using two-dimensional histograms. We propose both a uni-modal (based on first spatial derivative) and multi-modal (based on compositional data analysis) approach to this representation and quantify the benefits in 7 Tesla MRI data of nine volunteers. We present an openly accessible Python implementation of these approaches and demonstrate that editing cortical segmentations using two-dimensional histogram representations as an additional post-processing step aids existing algorithms and yields improved gray matter borders. By making our data and corresponding expert (ground truth) segmentations openly available, we facilitate future efforts to develop and test segmentation algorithms on this challenging type of data.

Cortical depth profiles of luminance contrast responses in human V1 and V2 using 7 T fMRI

Neural activity in early visual cortex is modulated by luminance contrast. Cortical depth (i.e., laminar) contrast responses have been studied in monkey early visual cortex, but not in humans. In addition to the high spatial resolution needed and the ensuing low signal-to-noise ratio, laminar studies in humans using fMRI are hampered by the strong venous vascular weighting of the fMRI signal. In this study, we measured luminance contrast responses in human V1 and V2 with high-resolution fMRI at 7 T. To account for the effect of intracortical ascending veins, we applied a novel spatial deconvolution model to the fMRI depth profiles. Before spatial deconvolution, the contrast response in V1 showed a slight local maximum at mid cortical depth, whereas V2 exhibited a monotonic signal increase toward the cortical surface. After applying the deconvolution, both V1 and V2 showed a pronounced local maximum at mid cortical depth, with an additional peak in deep grey matter, especially in V1. Moreover, we found a difference in contrast sensitivity between V1 and V2, but no evidence for variations in contrast sensitivity as a function of cortical depth. These findings are in agreement with results obtained in nonhuman primates, but further research will be needed to validate the spatial deconvolution approach.