Extensive topographic remapping and functional sharpening in the adult rat visual pathway upon first visual experience.

Understanding the dynamics of stability/plasticity balances during adulthood is pivotal for learning, disease, and recovery from injury. However, the brain-wide topography of sensory remapping remains unknown. Here, using a first-of-its-kind setup for delivering patterned visual stimuli in a rodent magnetic resonance imaging (MRI) scanner, coupled with biologically inspired computational models, we noninvasively mapped brain-wide properties-receptive fields (RFs) and spatial frequency (SF) tuning curves-that were insofar only available from invasive electrophysiology or optical imaging. We then tracked the RF dynamics in the chronic visual deprivation model (VDM) of plasticity and found that light exposure progressively promoted a large-scale topographic remapping in adult rats. Upon light exposure, the initially unspecialized visual pathway progressively evidenced sharpened RFs (smaller and more spatially selective) and enhanced SF tuning curves. Our findings reveal that visual experience following VDM reshapes both structure and function of the visual system and shifts the stability/plasticity balance in adults.

MP-PCA denoising of fMRI time-series data can lead to artificial activation "spreading".

MP-PCA denoising has become the method of choice for denoising MRI data since it provides an objective threshold to separate the signal components from unwanted thermal noise components. In rodents, thermal noise in the coils is an important source of noise that can reduce the accuracy of activation mapping in fMRI. Further confounding this problem, vendor data often contains zero-filling and other post-processing steps that may violate MP-PCA assumptions. Here, we develop an approach to denoise vendor data and assess activation "spreading" caused by MP-PCA denoising in rodent task-based fMRI data. Data was obtained from N = 3 mice using conventional multislice and ultrafast fMRI acquisitions (1 s and 50 ms temporal resolution, respectively), using a visual stimulation paradigm. MP-PCA denoising produced SNR gains of 64% and 39%, and Fourier Spectral Amplitude (FSA) increases in BOLD maps of 9% and 7% for multislice and ultrafast data, respectively, when using a small [2 2] denoising window. Larger windows provided higher SNR and FSA gains with increased spatial extent of activation that may or may not represent real activation. Simulations showed that MP-PCA denoising can incur activation "spreading" with increased false positive rate and smoother functional maps due to local "bleeding" of principal components, and that the optimal denoising window for improved specificity of functional mapping, based on Dice score calculations, depends on the data's tSNR and functional CNR. This "spreading" effect applies also to another recently proposed low-rank denoising method (NORDIC), although to a lesser degree. Our results bode well for enhancing spatial and/or temporal resolution in future fMRI work, while taking into account the sensitivity/specificity trade-offs of low-rank denoising methods.

A consensus protocol for functional connectivity analysis in the rat brain.

Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.

Intrinsic macroscale oscillatory modes driving long range functional connectivity in female rat brains detected by ultrafast fMRI.

Spontaneous fluctuations in functional magnetic resonance imaging (fMRI) signals correlate across distant brain areas, shaping functionally relevant intrinsic networks. However, the generative mechanism of fMRI signal correlations, and in particular the link with locally-detected ultra-slow oscillations, are not fully understood. To investigate this link, we record ultrafast ultrahigh field fMRI signals (9.4 Tesla, temporal resolution = 38 milliseconds) from female rats across three anesthesia conditions. Power at frequencies extending up to 0.3 Hz is detected consistently across rat brains and is modulated by anesthesia level. Principal component analysis reveals a repertoire of modes, in which transient oscillations organize with fixed phase relationships across distinct cortical and subcortical structures. Oscillatory modes are found to vary between conditions, resonating at faster frequencies under medetomidine sedation and reducing both in number, frequency, and duration with the addition of isoflurane. Peaking in power within clear anatomical boundaries, these oscillatory modes point to an emergent systemic property. This work provides additional insight into the origin of oscillations detected in fMRI and the organizing principles underpinning spontaneous long-range functional connectivity.

Soma and Neurite Density MRI (SANDI) of the in-vivo mouse brain and comparison with the Allen Brain Atlas.

Diffusion MRI (dMRI) provides unique insights into the neural tissue milieu by probing interactions between diffusing molecules and tissue microstructure. Most dMRI techniques focus on white matter (WM) tissues, nevertheless, interest in gray matter characterizations is growing. The Soma and Neurite Density MRI (SANDI) methodology harnesses a model incorporating water diffusion in spherical objects (assumed to be associated with cell bodies) and in impermeable "sticks" (assumed to represent neurites), which potentially enables the characterization of cellular and neurite densities. Recognising the importance of rodents in animal models of development, aging, plasticity, and disease, we here employ SANDI for in-vivo preclinical imaging and provide a first validation of the methodology by comparing SANDI metrics with cellular density reflected by the Allen mouse brain atlas. SANDI was implemented on a 9.4T scanner equipped with a cryogenic coil, and in-vivo experiments were carried out on N = 6 mice. Pixelwise, ROI-based, and atlas comparisons were performed, magnitude vs. real-valued analyses were compared, and shorter acquisitions with reduced the number of b-value shells were investigated. Our findings reveal good reproducibility of the SANDI parameters, including the sphere and stick fractions, as well as sphere size (CoV < 7%, 12% and 3%, respectively). Additionally, we find a very good rank correlation between SANDI-driven sphere fraction and Allen mouse brain atlas contrast that represents cellular density. We conclude that SANDI is a viable preclinical MRI technique that can greatly contribute to research on brain tissue microstructure.

Glucose fluxes in glycolytic and oxidative pathways detected in vivo by deuterium magnetic resonance spectroscopy reflect proliferation in mouse glioblastoma.

OBJECTIVES: Glioblastoma multiforme (GBM), the most aggressive glial brain tumors, can metabolize glucose through glycolysis and mitochondrial oxidation pathways. While specific dependencies on those pathways are increasingly associated with treatment response, detecting such GBM subtypes in vivo remains elusive. Here, we develop a dynamic glucose-enhanced deuterium spectroscopy (DGE 2H-MRS) approach for differentially assessing glucose turnover rates through glycolysis and mitochondrial oxidation in mouse GBM and explore their association with histologic features of the tumor and its microenvironment. MATERIALS AND METHODS: GL261 and CT2A glioma allografts were induced in immunocompetent mice and scanned in vivo at 9.4 Tesla, harnessing DGE 2H-MRS with volume selection and Marchenko-Pastur PCA (MP-PCA) denoising to achieve high temporal resolution. Each tumor was also classified by histopathologic analysis and assessed for cell proliferation (Ki67 immunostaining), while the respective cell lines underwent in situ extracellular flux analysis to assess mitochondrial function. RESULTS: MP-PCA denoising of in vivo DGE 2H-MRS data significantly improved the time-course detection (~2-fold increased Signal-to-Noise Ratio) and fitting precision (-19 ± 1 % Cramér-Rao Lower Bounds) of 2H-labelled glucose, and glucose-derived glutamate-glutamine (Glx) and lactate pools in GL261 and CT2A orthotopic tumors. Kinetic modeling further indicated inter-tumor heterogeneity of glucose consumption rate for glycolysis and oxidation during a defined epoch of active proliferation in both cohorts (19 ± 1 days post-induction), with consistent volumes (38.3 ± 3.4 mm3) and perfusion properties prior to marked necrosis. Histopathologic analysis of these tumors revealed clear differences in tumor heterogeneity between the two GBM models, aligned with metabolic differences of the respective cell lines monitored in situ. Importantly, glucose oxidation (i.e. Glx synthesis and elimination rates: 0.40 ± 0.08 and 0.12 ± 0.03 mM min-1, respectively) strongly correlated with cell proliferation across the pooled cohorts (R = 0.82, p = 0.001; and R = 0.80, p = 0.002, respectively), regardless of tumor morphologic features or in situ metabolic characteristics of each GBM model. CONCLUSIONS: Our fast DGE 2H-MRS enables the quantification of glucose consumption rates through glycolysis and mitochondrial oxidation in mouse GBM, which is relevant for assessing their modulation in vivo according to tumor microenvironment features such as cell proliferation. This novel application augurs well for non-invasive metabolic characterization of glioma or other cancers with mitochondrial oxidation dependencies.

Effective bowel motion reduction in mouse abdominal MRI using hyoscine butylbromide.

PURPOSE: Bowel motion is a significant source of artifacts in mouse abdominal MRI. Fasting and administration of hyoscine butylbromide (BUSC) have been proposed for bowel motion reduction but with inconsistent results and limited efficacy assessments. Here, we evaluate these regimes for mouse abdominal MRI at high field. METHODS: Thirty-two adult C57BL/6J mice were imaged on a 9.4T scanner with a FLASH sequence, acquired over 90 min with ~19 s temporal resolution. During MRI acquisition, 8 mice were injected with a low-dose and 8 mice with a high-dose bolus of BUSC (0.5 and 5 mg/kg, respectively). Eight mice were food deprived for 4.5-6.5 hours before MRI and another group of eight mice was injected with saline during MRI acquisition. Two expert readers reviewed the images and classified bowel motion, and quantitative voxel-wise analyses were performed for identification of moving regions. After defining the most effective protocol, high-resolution T2 -weighted and diffusion-weighted images were acquired from 4 mice. RESULTS: High-dose BUSC was the most effective protocol for bowel motion reduction, for up to 45 min. Fasting and saline protocols were not effective in suppressing bowel motion. High-resolution abdominal MRI clearly demonstrated improved image quality and ADC quantification with the high-dose BUSC protocol. CONCLUSION: Our data show that BUSC administration is advantageous for abdominal MRI in the mouse. Specifically, it endows significant bowel motion reduction, with relatively short onset timings after injection (~8.5 min) and relatively long duration of the effect (~45 min). These features improve the quality of high-resolution images of the mouse abdomen.

High temporal resolution functional magnetic resonance spectroscopy in the mouse upon visual stimulation.

Functional magnetic resonance spectroscopy (fMRS) quantifies metabolic variations upon presentation of a stimulus and can therefore provide complementary information compared to activity inferred from functional magnetic resonance imaging (fMRI). Improving the temporal resolution of fMRS can be beneficial to clinical applications where detailed information on metabolism can assist the characterization of brain function in healthy and sick populations as well as for neuroscience applications where information on the nature of the underlying activity could be potentially gained. Furthermore, fMRS with higher temporal resolution could benefit basic studies on animal models of disease and for investigating brain function in general. However, to date, fMRS has been limited to sustained periods of activation which risk adaptation and other undesirable effects. Here, we performed fMRS experiments in the mouse with high temporal resolution (12 s), and show the feasibility of such an approach for reliably quantifying metabolic variations upon activation. We detected metabolic variations in the superior colliculus of mice subjected to visual stimulation delivered in a block paradigm at 9.4 T. A robust modulation of glutamate is observed on the average time course, on the difference spectra and on the concentration distributions during active and recovery periods. A general linear model is used for the statistical analysis, and for exploring the nature of the modulation. Changes in NAAG, PCr and Cr levels were also detected. A control experiment with no stimulation reveals potential metabolic signal "drifts" that are not correlated with the functional activity, which should be taken into account when analyzing fMRS data in general. Our findings are promising for future applications of fMRS.

Neuroplasticity-driven timing modulations revealed by ultrafast functional magnetic resonance imaging.

Detecting neuroplasticity in global brain circuits in vivo is key for understanding myriad processes such as memory, learning, and recovery from injury. Functional Magnetic Resonance Imaging (fMRI) is instrumental for such in vivo mappings, yet it typically relies on mapping changes in spatial extent of activation or via signal amplitude modulations, whose interpretation can be highly ambiguous. Importantly, a central aspect of neuroplasticity involves modulation of neural activity timing properties. We thus hypothesized that this temporal dimension could serve as a new marker for neuroplasticity. To detect fMRI signals more associated with the underlying neural dynamics, we developed an ultrafast fMRI (ufMRI) approach facilitating high spatiotemporal sensitivity and resolution in distributed neural pathways. When neuroplasticity was induced in the mouse visual pathway via dark rearing, ufMRI indeed mapped temporal modulations in the entire visual pathway. Our findings therefore suggest a new dimension for exploring neuroplasticity in vivo.