An analysis approach for high-field fMRI data from awake non-human primates

Magnetization transfer weighted laminar fMRI with multi-echo FLASH

Laminar functional magnetic resonance imaging (fMRI) using the gradient echo (GRE) blood oxygenation level dependent (BOLD) contrast is prone to signal changes arising from large unspecific venous vessels. Alternatives based on changes of cerebral blood volume (CBV) become more popular since it is expected that this hemodynamic response is dominant in microvasculature. One approach to sensitize the signal toward changes in CBV, and to simultaneously reduce unwanted extravascular (EV) BOLD blurring, is to selectively reduce gray matter (GM) signal via magnetization transfer (MT). In this work, we use off-resonant MT-pulses with a 3D FLASH readout to perform MT-prepared (MT-prep) laminar fMRI of the primary visual cortex (V1) at multiple echo times at 7 T. With a GRE-BOLD contrast without additional MT-weighting as reference, we investigated the influence of the MT-preparation on the shape and the echo time dependency of laminar profiles. Through numerical simulations, we optimized the sequence parameters to increase the sensitivity toward signal changes induced by changes in arterial CBV and to delineate the contributions of different compartments to the signal. We show that at 7 T, GM signals can be reduced by 30 %. Our laminar fMRI responses exhibit an increased signal change in the parenchyma at very short TE compared to a BOLD-only reference as a result of reduced EV signal intensity. By varying echo times, we could show that MT-prep results in less sensitivity toward unwanted signal changes based on changes in T₂*. We conclude that when accounting for nuclear overhauser enhancement effects in blood, off-resonant MT-prep combined with efficient short TE readouts can become a promising method to reduce unwanted EV venous contributions in GRE-BOLD and/or to allow scanning at much shorter echo times without incurring a sensitivity penalty in laminar fMRI.

Laminar fMRI using T2-prepared multi-echo FLASH

Functional magnetic resonance imaging (fMRI) using blood oxygenation level dependent (BOLD) contrast at a sub-millimeter scale is a promising technique to probe neural activity at the level of cortical layers. While gradient echo (GRE) BOLD sequences exhibit the highest sensitivity, their signal is confounded by unspecific extravascular (EV) and intravascular (IV) effects of large intracortical ascending veins and pial veins leading to a downstream blurring effect of local signal changes. In contrast, spin echo (SE) fMRI promises higher specificity towards signal changes near the microvascular compartment. However, the T₂-weighted signal is typically sampled with a gradient echo readout imposing additional T₂'-weighting. In this work, we used a T₂-prepared (T₂-prep) sequence with short GRE readouts to investigate its capability to acquire laminar fMRI data during a visual task in humans at 7 T. By varying the T₂-prep echo time (TE_prep) and acquiring multiple gradient echoes (TE_GRE) per excitation, we studied the specificity of the sequence and the influence of possible confounding contributions to the shape of laminar fMRI profiles. By fitting and extrapolating the multi-echo GRE data to a TE_GRE = 0 ms condition, we show for the first time laminar profiles free of T₂'-pollution, confined to gray matter. This finding is independent of TE_prep, except for the shortest one (31 ms) where hints of a remaining intravascular component can be seen. For TE_GRE > 0 ms a prominent peak at the pial surface is observed that increases with longer TE_GRE and dominates the shape of the profiles independent of the amount of T₂-weighting. Simulations show that the peak at the pial surface is a result of static EV dephasing around pial vessels in CSF visible in GM due to partial voluming. Additionally, another, weaker, static dephasing effect is observed throughout all layers of the cortex, which is particularly obvious in the data with shortest T₂-prep echo time. Our simulations show that this cannot be explained by intravascular dephasing but that it is likely caused by extravascular effects of the intracortical and pial veins. We conclude that even for TE_GRE as short as 2.3 ms, the T₂'-weighting added to the T₂-weighting is enough to dramatically affect the laminar specificity of the BOLD signal change. However, the bulk of this corruption stems from CSF partial volume effects which can in principle be addressed by increasing the spatial resolution of the acquisition.

A Hitchhiker's Guide to Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging (fMRI) studies have become increasingly popular both with clinicians and researchers as they are capable of providing unique insights into brain functions. However, multiple technical considerations (ranging from specifics of paradigm design to imaging artifacts, complex protocol definition, and multitude of processing and methods of analysis, as well as intrinsic methodological limitations) must be considered and addressed in order to optimize fMRI analysis and to arrive at the most accurate and grounded interpretation of the data. In practice, the researcher/clinician must choose, from many available options, the most suitable software tool for each stage of the fMRI analysis pipeline. Herein we provide a straightforward guide designed to address, for each of the major stages, the techniques, and tools involved in the process. We have developed this guide both to help those new to the technique to overcome the most critical difficulties in its use, as well as to serve as a resource for the neuroimaging community.

Scent of the familiar: an fMRI study of canine brain responses to familiar and unfamiliar human and dog odors

Understanding dogs' perceptual experience of both conspecifics and humans is important to understand how dogs evolved and the nature of their relationships with humans and other dogs. Olfaction is believed to be dogs' most powerful and perhaps important sense and an obvious place to begin for the study of social cognition of conspecifics and humans. We used fMRI in a cohort of dogs (N=12) that had been trained to remain motionless while unsedated and unrestrained in the MRI. By presenting scents from humans and conspecifics, we aimed to identify the dimensions of dogs' responses to salient biological odors - whether they are based on species (dog or human), familiarity, or a specific combination of factors. We focused our analysis on the dog's caudate nucleus because of its well-known association with positive expectations and because of its clearly defined anatomical location. We hypothesized that if dogs' primary association to reward, whether it is based on food or social bonds, is to humans, then the human scents would activate the caudate more than the conspecific scents. Conversely, if the smell of conspecifics activated the caudate more than the smell of humans, dogs' association to reward would be stronger to their fellow canines. Five scents were presented (self, familiar human, strange human, familiar dog, strange dog). While the olfactory bulb/peduncle was activated to a similar degree by all the scents, the caudate was activated maximally to the familiar human. Importantly, the scent of the familiar human was not the handler, meaning that the caudate response differentiated the scent in the absence of the person being present. The caudate activation suggested that not only did the dogs discriminate that scent from the others, they had a positive association with it. This speaks to the power of the dog's sense of smell, and it provides important clues about the importance of humans in dogs' lives. This article is part of a Special Issue entitled: Canine Behavior.

The helmet head restraint system: a viable solution for resting state fMRI in awake monkeys

In monkey neuroimaging, head restraint is currently achieved via surgical implants. Eradicating such invasive head restraint from otherwise non-invasive monkey studies could represent a substantial progress in terms of Reduction and Refinement. Two non-invasive helmet-based methods are available but they are used exclusively by the pioneering research groups who designed them. In the absence of independent replication, they have had little impact in replacing the surgical implants. Here, we built a modified version of the helmet system proposed by Srihasam et al. (2010 NeuroImage, 51(1), 267-73) and tested it for resting state fMRI in awake monkeys. Extremely vulnerable to motion artifacts, resting state fMRI represents a decisive test for non-invasive head restraint systems. We compared two monkeys restrained with the helmet to one monkey with a surgically implanted head post using both a seed-based approach and an independent component analysis. Technically, the helmet system proved relatively easy to develop. Scientifically, although it allowed more extensive movements than the head post system, the helmet proved viable for resting state fMRI, in particular when combined with the independent component analysis that deals more effectively with movement-related noise than the seed-based approach. We also discuss the pros and cons of such device in light of the European Union new 2013 regulation on non-human primate research and its firm Reduction and Refinement requests.

Functional MRI in awake unrestrained dogs

Because of dogs' prolonged evolution with humans, many of the canine cognitive skills are thought to represent a selection of traits that make dogs particularly sensitive to human cues. But how does the dog mind actually work? To develop a methodology to answer this question, we trained two dogs to remain motionless for the duration required to collect quality fMRI images by using positive reinforcement without sedation or physical restraints. The task was designed to determine which brain circuits differentially respond to human hand signals denoting the presence or absence of a food reward. Head motion within trials was less than 1 mm. Consistent with prior reinforcement learning literature, we observed caudate activation in both dogs in response to the hand signal denoting reward versus no-reward.