acquisition-resting-state-functional-magnetic-resonance-imaging-data

Acquisition of Resting-State Functional Magnetic Resonance Imaging Data in the Rat

Resting-state functional magnetic resonance imaging (rs-fMRI) has become an increasingly popular method to study brain function in a resting, non-task ...

Geisel School of Medicine at Dartmouth

National Institutes of Health

In cerebral blood volume (CBV)-weighted functional MRI (fMRI) employing superparamagnetic contrast agent, iron dose and blood oxygenation level dependent (BOLD) contamination are two important issues for experimental design and CBV quantification. Both BOLD and CBV-weighted fMRI are based upon the susceptibility effect, to which spin-echo and gradient-echo sequences have different sensitivities. In the present study, CBV-weighted fMRI was conducted using spin-echo and gradient-echo sequences at 9.4T by systematically changing the doses of contrast agent. Results suggest that BOLD contamination is a significant component in CBV-weighted fMRI at high field, particularly when relatively low dose of contrast agent is administered. A mathematical model was developed to quantify the extravascular (EV) BOLD effect. With a TE of 35 ms, the EV BOLD effect was estimated to account for 76+/-12% of the observed spin-echo fMRI signal at 9.4T. These data suggest that correcting BOLD effect may be necessary for accurately quantifying activation-induced CBV changes at high field.

Quantifying the blood oxygenation level dependent effect in cerebral blood volume-weighted functional MRI at 9.4T.

In pharmacological magnetic resonance imaging (phMRI) with anesthetized animals, there is usually only a single time window to observe the dynamic signal change to an acute drug administration since subsequent drug injections are likely to result in altered response properties (e.g., tolerance). Unlike the block-design experiments in which fMRI signal can be elicited with multiple repetitions of a task, these single-event experiments require stable baseline in order to reliably identify drug-induced signal changes. Such factors as subject motion, scanner instability and/or alterations in physiological conditions of the anesthetized animal could confound the baseline signal. The unique feature of such functional MRI (fMRI) studies necessitates a technique that is able to monitor MRI signal in a real-time fashion and to interactively control certain experimental procedures. In the present study, an approach for real-time MRI on a Bruker scanner is presented. The custom software runs on the console computer in parallel with the scanner imaging software, and no additional hardware is required. The utility of this technique is demonstrated in manganese-enhanced MRI (MEMRI) with acute cocaine challenge, in which temporary disruption of the blood-brain barrier (BBB) is a critical step for MEMRI experiments. With the aid of real-time MRI, we were able to assess the outcome of BBB disruption following bolus injection of hyperosmolar mannitol in a near real-time fashion prior to drug administration, improving experimental success rate. It is also shown that this technique can be applied to monitor baseline physiological conditions in conventional fMRI experiments using blood oxygenation level-dependent (BOLD) contrast, further demonstrating the versatility of this technique.

Real-time animal functional magnetic resonance imaging and its application to neuropharmacological studies.

The value of analyzing neuroimaging data on a group level has been well established in human studies. However, there is no standard procedure for registering and analyzing functional magnetic resonance imaging (fMRI) data into common space in rodent fMRI studies. An approach for performing rat imaging data analysis in the stereotaxic framework is presented. This method is rooted in the biological observation that the skull shape and size of rat brain are essentially the same as long as their weights are within certain range. Registration is performed using rigid-body transformations without scaling or shearing, preserving the unique properties of the stable shape and size inherent in rat brain structure. Also, it does not require brain tissue masking and is not biased towards surface coil sensitivity profile. A standard rat brain atlas is used to facilitate the identification of activated areas in common space, allowing accurate region of interest analysis. This technique is evaluated from a group of rats (n=11) undergoing routine MRI scans; the registration accuracy is estimated to be within 400 microm. The analysis of fMRI data acquired with an electrical forepaw stimulation model demonstrates the utility of this technique. The method is implemented within the Analysis of Functional NeuroImages (AFNI) framework and can be readily extended to other studies.

Registering and analyzing rat fMRI data in the stereotaxic framework by exploiting intrinsic anatomical features.

In quantitative perfusion imaging using arterial spin labeling, variable blood transit times and postlabeling delays are two confounding factors that may compromise the accuracy of perfusion quantifications. In this study, theoretical analyses and experimental data at 9.4 T demonstrate that increasing labeling duration not only enhances the contrast of the arterial spin labeling signal but also minimizes the effect of variable postlabeling delays in multislice arterial spin labeling acquisitions. With a labeling duration of 6.4 sec, arterial spin labeling signal acquired in multislice mode (11 slices) is very similar to that acquired in single-slice mode. Previous studies have shown that inserting a delay between the spin labeling pulse and the image acquisition pulse could reduce confounds resulting from variable blood transit times at the expense of arterial spin labeling sensitivity. Our simulations suggest that enhancing the contrast of arterial spin labeling signal offers the opportunity for extending the postlabeling delay to a longer duration, minimizing systematic errors associated with a wide range of blood transit times, which could have significant implications for applying arterial spin labeling techniques to perfusion imaging of pathological conditions in animal models.

High-field continuous arterial spin labeling with long labeling duration: reduced confounds from blood transit time and postlabeling delay.

Anesthetics are commonly used in preclinical functional MRI studies. It is well-appreciated that proper choice of anesthetics is of critical importance for maintaining a physiologically normal range of autonomic functioning. A recent study, using a low dose of dexmedetomidine (active isomer of medetomidine) in combination with a low dose of isoflurane, suggested stable measurements across repeated fMRI experiments in individual animals with each session lasting up to several hours. The rat default mode network has been successfully identified using this preparation, indicating that this protocol minimally disturbs brain network functions. However, medetomidine is known to cause peripheral vasoconstriction, respiratory suppression, and bradycardia, each of which could independently confound the BOLD signal. The goal of this study was to systematically characterize physiological conditions for fMRI experiments under this anesthetic regimen. To this end, we acquired somatosensory stimulation "task-evoked" and resting-state fMRI to evaluate the integrity of neurovascular coupling and brain network function during three time windows (0-30min, 30-90min, and 90-150min) following dexmedetomidine initiation. Results demonstrate that both evoked BOLD response and resting-state fMRI signal remained stable during the 90-150min time window, while autonomic physiological parameters maintained near-normal conditions during this period. Our data suggest that using a spontaneously-inhaled, low dose of isoflurane in combination with a continuous low dose of dexmedetomidine is a viable option for longitudinal imaging studies in rats.

Physiological characterization of a robust survival rodent fMRI method.

Characterizing the nature and underlying neurobiological causes of psychiatric and neurological diseases at the circuit and network levels has remained elusive and necessitates the use of robust animal models. Noninvasive functional magnetic resonance imaging allows systems-level insight into disease phenotype in humans and animals alike, and functional neuroimaging represents an ideal platform for translational and reverse-translational research, with common measurements collected across species. Animal neuroimaging allows invasive manipulations and conveniently bypasses many limitations associated with human subjects; however, awake animal imaging introduces its own constraints to reduce motion and limit subjective stress. Anesthetics offer a viable alternative, but the pharmacodynamics, pharmacokinetics, and molecular targets of anesthetics and their effects on physiology, neural activity, and neurovascular coupling must be considered. We discuss the physiological basis of and the influence of anesthetics on neurovascular coupling. We discuss anesthetic use in functional magnetic resonance imaging and focus on an anesthetic protocol developed in our laboratory. Finally, we discuss in detail our most recent work examining the physiological basis of resting-state functional magnetic resonance imaging using this anesthetic regimen and the future directions of animal neuroimaging research. Using animal imaging in combination with cutting-edge in vivo neuromodulatory techniques is essential for causal understanding of brain function in health and disease and offers an exemplary bridge between human and animal research studies.

Article	Year
Quantifying the blood oxygenation level dependent effect in cerebral blood volume-weighted functional MRI at 9.4T. Magnetic resonance in medicine\| PubMed ID: 17763339	2007
Real-time animal functional magnetic resonance imaging and its application to neuropharmacological studies. Magnetic resonance imaging\| PubMed ID: 18448300	2008
Registering and analyzing rat fMRI data in the stereotaxic framework by exploiting intrinsic anatomical features. Magnetic resonance imaging\| PubMed ID: 19608368	2010
High-field continuous arterial spin labeling with long labeling duration: reduced confounds from blood transit time and postlabeling delay. Magnetic resonance in medicine\| PubMed ID: 20715292	2010
Physiological characterization of a robust survival rodent fMRI method. Magnetic resonance imaging\| PubMed ID: 27580522	2017
Physiological Considerations of Functional Magnetic Resonance Imaging in Animal Models. Biological psychiatry. Cognitive neuroscience and neuroimaging\| PubMed ID: 30270095	2019

Hanbing Lu

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