In vivo measurement of T1 and T2 relaxation times in awake pigeon and rat brains at 7T

Estimating the volume of penumbra in rodents using DTI and stack-based ensemble machine learning framework

BACKGROUND

This study investigates the potential of diffusion tensor imaging (DTI) in identifying penumbral volume (PV) compared to the standard gadolinium-required perfusion-diffusion mismatch (PDM), utilizing a stack-based ensemble machine learning (ML) approach with enhanced explainability.

METHODS

Sixteen male rats were subjected to middle cerebral artery occlusion. The penumbra was identified using PDM at 30 and 90 min after occlusion. We used 11 DTI-derived metrics and 14 distance-based features to train five voxel-wise ML models. The model predictions were integrated using stack-based ensemble techniques. ML-estimated and PDM-defined PVs were compared to evaluate model performance through volume similarity assessment, the Pearson correlation analysis, and Bland-Altman analysis. Feature importance was determined for explainability.

RESULTS

In the test rats, the ML-estimated median PV was 106.4 mL (interquartile range 44.6-157.3 mL), whereas the PDM-defined median PV was 102.0 mL (52.1-144.9 mL). These PVs had a volume similarity of 0.88 (0.79-0.96), a Pearson correlation coefficient of 0.93 (p < 0.001), and a Bland-Altman bias of 2.5 mL (2.4% of the mean PDM-defined PV), with 95% limits of agreement ranging from -44.9 to 49.9 mL. Among the features used for PV prediction, the mean diffusivity was the most important feature.

CONCLUSIONS

Our study confirmed that PV can be estimated using DTI metrics with a stack-based ensemble ML approach, yielding results comparable to the volume defined by the standard PDM. The model explainability enhanced its clinical relevance. Human studies are warranted to validate our findings.

RELEVANCE STATEMENT

The proposed DTI-based ML model can estimate PV without the need for contrast agent administration, offering a valuable option for patients with kidney dysfunction. It also can serve as an alternative if perfusion map interpretation fails in the clinical setting.

KEY POINTS

• Penumbral volume can be estimated by DTI combined with stack-based ensemble ML. • Mean diffusivity was the most important feature used for predicting penumbral volume. • The proposed approach can be beneficial for patients with kidney dysfunction.

Segmented spin-echo echo-planar imaging improves whole-brain BOLD functional MRI in awake pigeon brains

Functional magnetic resonance imaging (fMRI) in awake small animals such as pigeons or songbirds opens a new window into the neural fundaments of cognitive behavior. However, high-field fMRI in the avian brain is challenging due to strong local magnetic field inhomogeneities caused by air cavities in the skull. A spoiled gradient-echo fMRI sequence has already been used to map the auditory network in songbirds, but due to susceptibility artifacts only 50% of the whole brain could be recorded. Since whole-brain fMRI coverage is vital to reveal whole-brain networks, an MRI sequence that is less susceptible to these artifacts was required. This was recently achieved in various bird species by using a rapid acquisition with relaxation enhancement (RARE) sequence. Weak blood oxygen level-dependent (BOLD) sensitivity, low temporal resolution, and heat caused by the long train of RF refocusing pulses are the main limits of RARE fMRI at high magnetic fields. To go beyond some of these limitations, we here describe the implementation of a two-segmented spin-echo echo-planar imaging (SE-EPI). The proposed sequence covers the whole brain of awake pigeons. The sequence was applied to investigate the auditory network in awake pigeons and assessed the relative merits of this method in comparison with the single-shot RARE sequence. At the same imaging resolution but with a volume acquisition of 3 s versus 4 s for RARE, the two-segmented SE-EPI provided twice the strength of BOLD activity compared with the single-shot RARE sequence, while the image signal-to-noise ratio (SNR) and in particular the temporal SNR were very similar for the two sequences. In addition, the activation patterns in two-segmented SE-EPI data are more symmetric and larger than single-shot RARE results. Two-segmented SE-EPI represents a valid alternative to the RARE sequence in avian fMRI research since it yields more than twice the BOLD sensitivity per unit of time with much less energy deposition and better temporal resolution, particularly for event-related experiments.

Wide-spread brain activation and reduced CSF flow during avian REM sleep

Mammalian sleep has been implicated in maintaining a healthy extracellular environment in the brain. During wakefulness, neuronal activity leads to the accumulation of toxic proteins, which the glymphatic system is thought to clear by flushing cerebral spinal fluid (CSF) through the brain. In mice, this process occurs during non-rapid eye movement (NREM) sleep. In humans, ventricular CSF flow has also been shown to increase during NREM sleep, as visualized using functional magnetic resonance imaging (fMRI). The link between sleep and CSF flow has not been studied in birds before. Using fMRI of naturally sleeping pigeons, we show that REM sleep, a paradoxical state with wake-like brain activity, is accompanied by the activation of brain regions involved in processing visual information, including optic flow during flight. We further demonstrate that ventricular CSF flow increases during NREM sleep, relative to wakefulness, but drops sharply during REM sleep. Consequently, functions linked to brain activation during REM sleep might come at the expense of waste clearance during NREM sleep.

Validation of a New Coil Array Tailored for Dog Functional Magnetic Resonance Imaging Studies

Comparative neuroimaging allows for the identification of similarities and differences between species. It provides an important and promising avenue, to answer questions about the evolutionary origins of the brain´s organization, in terms of both structure and function. Dog functional magnetic resonance imaging (fMRI) has recently become one particularly promising and increasingly used approach to study brain function and coevolution. In dog neuroimaging, image acquisition has so far been mostly performed with coils originally developed for use in human MRI. Since such coils have been tailored to human anatomy, their sensitivity and data quality is likely not optimal for dog MRI. Therefore, we developed a multichannel receive coil (K9 coil, read "canine") tailored for high-resolution functional imaging in canines, optimized for dog cranial anatomy. In this paper we report structural (n = 9) as well as functional imaging data (resting-state, n = 6; simple visual paradigm, n = 9) collected with the K9 coil in comparison to reference data collected with a human knee coil. Our results show that the K9 coil significantly outperforms the human knee coil, improving the signal-to-noise ratio (SNR) across the imaging modalities. We noted increases of roughly 45% signal-to-noise in the structural and functional domain. In terms of translation to fMRI data collected in a visual flickering checkerboard paradigm, group-level analyses show that the K9 coil performs better than the knee coil as well. These findings demonstrate how hardware improvements may be instrumental in driving data quality, and thus, quality of imaging results, for dog-human comparative neuroimaging.

Multiparametric MRI enables for differentiation of different degrees of malignancy in two murine models of breast cancer

Objective

The objective of this study was to non-invasively differentiate the degree of malignancy in two murine breast cancer models based on identification of distinct tissue characteristics in a metastatic and non-metastatic tumor model using a multiparametric Magnetic Resonance Imaging (MRI) approach.

Methods

The highly metastatic 4T1 breast cancer model was compared to the non-metastatic 67NR model. Imaging was conducted on a 9.4 T small animal MRI. The protocol was used to characterize tumors regarding their structural composition, including heterogeneity, intratumoral edema and hemorrhage, as well as endothelial permeability using apparent diffusion coefficient (ADC), T1/T2 mapping and dynamic contrast-enhanced (DCE) imaging. Mice were assessed on either day three, six or nine, with an i.v. injection of the albumin-binding contrast agent gadofosveset. Ex vivo validation of the results was performed with laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), histology, immunhistochemistry and electron microscopy.

Results

Significant differences in tumor composition were observed over time and between 4T1 and 67NR tumors. 4T1 tumors showed distorted blood vessels with a thin endothelial layer, resulting in a slower increase in signal intensity after injection of the contrast agent. Higher permeability was further reflected in higher K_trans values, with consecutive retention of gadolinium in the tumor interstitium visible in MRI. 67NR tumors exhibited blood vessels with a thicker and more intact endothelial layer, resulting in higher peak enhancement, as well as higher maximum slope and area under the curve, but also a visible wash-out of the contrast agent and thus lower K_trans values. A decreasing accumulation of gadolinium during tumor progression was also visible in both models in LA-ICP-MS. Tissue composition of 4T1 tumors was more heterogeneous, with intratumoral hemorrhage and necrosis and corresponding higher T1 and T2 relaxation times, while 67NR tumors mainly consisted of densely packed tumor cells. Histogram analysis of ADC showed higher values of mean ADC, histogram kurtosis, range and the 90^th percentile (p90), as markers for the heterogenous structural composition of 4T1 tumors. Principal component analysis (PCA) discriminated well between the two tumor models.

Conclusions

Multiparametric MRI as presented in this study enables for the estimation of malignant potential in the two studied tumor models via the assessment of certain tumor features over time.

Noninvasive ultrasonic induction of cerebrospinal fluid flow enhances intrathecal drug delivery

Intrathecal drug delivery is routinely used in the treatment and prophylaxis of varied central nervous system conditions, as doing so allows drugs to directly bypass the blood-brain barrier. However, the utility of this route of administration is limited by poor brain and spinal cord parenchymal drug uptake from the cerebrospinal fluid. We demonstrate that a simple noninvasive transcranial ultrasound protocol can significantly increase influx of cerebrospinal fluid into the perivascular spaces of the brain, to enhance the uptake of intrathecally administered drugs. Specifically, we administered small (~1 kDa) and large (~155 kDa) molecule agents into the cisterna magna of rats and then applied low, diagnostic-intensity focused ultrasound in a scanning protocol throughout the brain. Using real-time magnetic resonance imaging and ex vivo histologic analyses, we observed significantly increased uptake of small molecule agents into the brain parenchyma, and of both small and large molecule agents into the perivascular space from the cerebrospinal fluid. Notably, there was no evidence of brain parenchymal damage following this intervention. The low intensity and noninvasive approach of transcranial ultrasound in this protocol underscores the ready path to clinical translation of this technique. In this manner, this protocol can be used to directly bypass the blood-brain barrier for whole-brain delivery of a variety of agents. Additionally, this technique can potentially be used as a means to probe the causal role of the glymphatic system in the variety of disease and physiologic processes to which it has been correlated.

Gradual Restraint Habituation for Awake Functional Magnetic Resonance Imaging Combined With a Sparse Imaging Paradigm Reduces Motion Artifacts and Stress Levels in Rodents

Functional magnetic resonance imaging, as a non-invasive technique, offers unique opportunities to assess brain function and connectivity under a broad range of applications, ranging from passive sensory stimulation to high-level cognitive abilities, in awake animals. This approach is confounded, however, by the fact that physical restraint and loud unpredictable acoustic noise must inevitably accompany fMRI recordings. These factors induce marked stress in rodents, and stress-related elevations of corticosterone levels are known to alter information processing and cognition in the rodent. Here, we propose a habituation strategy that spans specific stages of adaptation to restraint, MRI noise, and confinement stress in awake rats and circumvents the need for surgical head restraint. This habituation protocol results in stress levels during awake fMRI that do not differ from pre-handling levels and enables stable image acquisition with very low motion artifacts. For this, rats were gradually trained over a period of three weeks and eighteen training sessions. Stress levels were assessed by analysis of fecal corticosterone metabolite levels and breathing rates. We observed significant drops in stress levels to below pre-handling levels at the end of the habituation procedure. During fMRI in awake rats, after the conclusion of habituation and using a non-invasive head-fixation device, breathing was stable and head motion artifacts were minimal. A task-based fMRI experiment, using acoustic stimulation, conducted 2 days after the end of habituation, resulted in precise whole brain mapping of BOLD signals in the brain, with clear delineation of the expected auditory-related structures. The active discrimination by the animals of the acoustic stimuli from the backdrop of scanner noise was corroborated by significant increases in BOLD signals in the thalamus and reticular formation. Taken together, these data show that effective habituation to awake fMRI can be achieved by gradual and incremental acclimatization to the experimental conditions. Subsequent BOLD recordings, even during superimposed acoustic stimulation, reflect low stress-levels, low motion and a corresponding high-quality image acquisition. Furthermore, BOLD signals obtained during fMRI indicate that effective habituation facilitates selective attention to sensory stimuli that can in turn support the discrimination of cognitive processes in the absence of stress confounds.

Event-related functional MRI of awake behaving pigeons at 7T

Animal-fMRI is a powerful method to understand neural mechanisms of cognition, but it remains a major challenge to scan actively participating small animals under low-stress conditions. Here, we present an event-related functional MRI platform in awake pigeons using single-shot RARE fMRI to investigate the neural fundaments for visually-guided decision making. We established a head-fixated Go/NoGo paradigm, which the animals quickly learned under low-stress conditions. The animals were motivated by water reward and behavior was assessed by logging mandibulations during the fMRI experiment with close to zero motion artifacts over hundreds of repeats. To achieve optimal results, we characterized the species-specific hemodynamic response function. As a proof-of-principle, we run a color discrimination task and discovered differential neural networks for Go-, NoGo-, and response execution-phases. Our findings open the door to visualize the neural fundaments of perceptual and cognitive functions in birds-a vertebrate class of which some clades are cognitively on par with primates.

A Multicenter Preclinical MRI Study: Definition of Rat Brain Relaxometry Reference Maps

Similarly to human population imaging, there are several well-founded motivations for animal population imaging, the most notable being the improvement of the validity of statistical results by pooling a sufficient number of animal data provided by different imaging centers. In this paper, we demonstrate the feasibility of such a multicenter animal study, sharing raw data from forty rats and processing pipelines between four imaging centers. As specific use case, we focused on T1 and T2 mapping of the healthy rat brain at 7T. We quantitatively report about the variability observed across two MR data providers and evaluate the influence of image processing steps on the final maps, using three fitting algorithms from three centers. Finally, to derive relaxation times from different brain areas, two multi-atlas segmentation pipelines from different centers were performed on two different platforms. Differences between the two data providers were 2.21% for T1 and 9.52% for T2. Differences between processing pipelines were 1.04% for T1 and 3.33% for T2. These maps, obtained in healthy conditions, may be used in the future as reference when exploring alterations in animal models of pathology.

An in vivo proton magnetic resonance spectroscopy study with optimized echo-time technique for concurrent quantification and T2 measurement targeting glutamate in the rat brain

OBJECTIVE

The present study applied in vivo proton magnetic resonance spectroscopy (¹H MRS) to concurrently measure the concentration and T2 relaxation time of glutamate with the concept of optimized-for-quantification-and-T2-measurement-of-glutamate (OpQT2-Glu).

MATERIALS AND METHODS

7T MRS scans of the OpQT2-Glu were acquired from the prefrontal cortex of five rats. The echo-time-(TE)-specific J-modulation of glutamate was investigated by spectral simulations and analyses for selecting the eight TEs appropriate for T2 estimation of glutamate. The OpQT2-Glu results were compared to those of the typical short-TE MRS and T2 measurements.

RESULTS

No significant differences were observed between the OpQT2-Glu and typical short-TE MRS (p > 0.050). The estimated glutamate T2 (67.75 ms) of the OpQT2-Glu was similar to the multiple TE MRS for the T2 measurement (71.58 ms) with enhanced signal-to-noise ratio and reliability.

DISCUSSION

The results revealed that the quantification reliability of the OpQT2-Glu was comparable to that of the single short-TE MRS and its estimation reliability for the T2 relaxation time of glutamate was enhanced compared to the multiple TE MRS for T2 measurement. Despite certain limitations, the quantification and T2 estimation of glutamate can be concurrently performed within an acceptable scan time via high-field in vivo ¹H MRS with the OpQT2-Glu.

A three-dimensional digital atlas of the Nile crocodile (Crocodylus niloticus) forebrain

The phylogenetic position of crocodilians in relation to birds and mammals makes them an interesting animal model for investigating the evolution of the nervous system in amniote vertebrates. A few neuroanatomical atlases are available for reptiles, but with a growing interest in these animals within the comparative neurosciences, a need for these anatomical reference templates is becoming apparent. With the advent of MRI being used more frequently in comparative neuroscience, the aim of this study was to create a three-dimensional MRI-based atlas of the Nile crocodile (Crocodylus niloticus) brain to provide a common reference template for the interpretation of the crocodilian, and more broadly reptilian, brain. Ex vivo MRI acquisitions in combination with histological data were used to delineate crocodilian brain areas at telencephalic, diencephalic, mesencephalic, and rhombencephalic levels. A total of 50 anatomical structures were successfully identified and outlined to create a 3-D model of the Nile crocodile brain. The majority of structures were more readily discerned within the forebrain of the crocodile with the methods used to produce this atlas. The anatomy outlined herein corresponds with both classical and recent crocodilian anatomical analyses, barring a few areas of contention predominantly related to a lack of functional data and conflicting nomenclature.

Detecting sub-voxel microvasculature with USPIO-enhanced susceptibility-weighted MRI at 7 T

BACKGROUND

Susceptibility weighted imaging (SWI) combines phase with magnitude information to better image sub-voxel veins. Recently, it has been extended to image very small sub-voxel arteries and veins by injecting intravenously the ultra-small superparamagnetic iron oxide, Ferumoxytol.

OBJECTIVE

To determine practical experimental imaging parameters for sub-voxel cerebral vessels at 7 T.

METHODS

Six Wistar-Kyoto rats aged 7-13 weeks were imaged. For a given spatial resolution, SWI was acquired pre- and post- Ferumoxytol with doses of 2, 4, 6 and 8 mg/kg and echo times (TEs) of 5, 10 and 15 ms at each dose. The spatial resolutions of 62.5 × 125 × 250 μm³ (acquisition time of 7.5 min) and 62.5 × 62.5 × 125 μm³ (30 min) were used. Both SWI and quantitative susceptibility mapping (QSM) data were analyzed. Contrast-to-noise ratio (CNR) was measured and used to determine the optimal practical imaging parameters for detection of small cortical penetrating arteries.

RESULTS

For a given spatial resolution with an aspect ratio (frequency: phase: slice) of 2:4:8 relative to the vessel size, we found the TE-dose index (TE x dose) must be at least 40 ms·mg/kg for both SWI and QSM to reveal the most vessels. The higher the TE-dose index, the better the image quality for both SWI and QSM up to 60 ms·mg/kg.

CONCLUSIONS

There is an optimal TE-dose index for improved visualization of sub-voxel vessels. Choosing the smallest TE and the largest allowed dose made it possible to run the sequence efficiently. In practice, the aspect ratio of 2:4:8 and the TE-dose index ranging from 40 to 60 ms·mg/kg provided the optimal and most practical solution.

Behavioral neuroimaging in birds using PET

BACKGROUND

Birds comprise the most diverse group of terrestrial vertebrates. This success likely is related to the evolution of powered flight over 75 mya. Modern approaches for studying brain function, however, have yet to be fully adapted and applied to birds, especially as they relate to specific behaviors including flight. New method: We have developed a comprehensive set of in vivo experimental methods utilizing PET imaging with F-18 labeled fluorodeoxyglucose (FDG) to study regional changes in metabolism specifically related to flight, yet applicable to other behaviors as well. It incorporates approaches for selection of species, behavioral/imaging paradigm, animal preparation, radiotracer injection route, image quantification, and image analysis via an enhanced brain atlas. We also carried out preliminary modeling studies to better understand tracer kinetics.

RESULTS

The methods were successful in identifying brain regions statistically associated with flight using only 8 animals. Peak brain uptake of FDG between birds and rodents is similar despite much higher blood glucose levels in birds. We also confirmed that brain uptake of FDG steadily decreases after the initial peak and provide evidence that it may be related to greater dephosphorylation of FDG phosphate than that observed in mammals. Comparison with existing methods: FDG PET has been used in only a few studies of the bird brain. We introduce a new species, more realistic flight behavior, paired (test/retest) design, and improved quantification and analysis approaches.

CONCLUSIONS

The proposed imaging protocol is non-invasive yet sensitive to regional metabolic changes in the bird brain related to behavior.

Functional MRI in the Nile crocodile: a new avenue for evolutionary neurobiology

Crocodilians are important for understanding the evolutionary history of amniote neural systems as they are the nearest extant relatives of modern birds and share a stem amniote ancestor with mammals. Although the crocodilian brain has been investigated anatomically, functional studies are rare. Here, we employed functional magnetic resonance imaging (fMRI), never tested in poikilotherms, to investigate crocodilian telencephalic sensory processing. Juvenile Crocodylus niloticus were placed in a 7 T MRI scanner to record blood oxygenation level-dependent (BOLD) signal changes during the presentation of visual and auditory stimuli. Visual stimulation increased BOLD signals in rostral to mid-caudal portions of the dorso-lateral anterior dorsal ventricular ridge (ADVR). Simple auditory stimuli led to signal increase in the rostromedial and caudocentral ADVR. These activation patterns are in line with previously described projection fields of diencephalic sensory fibres. Furthermore, complex auditory stimuli activated additional regions of the caudomedial ADVR. The recruitment of these additional, presumably higher-order, sensory areas reflects observations made in birds and mammals. Our results indicate that structural and functional aspects of sensory processing have been likely conserved during the evolution of sauropsids. In addition, our study shows that fMRI can be used to investigate neural processing in poikilotherms, providing a new avenue for neurobiological research in these critical species.