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1.
Science ; 384(6696): eadm7168, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38723062

ABSTRACT

Despite a half-century of advancements, global magnetic resonance imaging (MRI) accessibility remains limited and uneven, hindering its full potential in health care. Initially, MRI development focused on low fields around 0.05 Tesla, but progress halted after the introduction of the 1.5 Tesla whole-body superconducting scanner in 1983. Using a permanent 0.05 Tesla magnet and deep learning for electromagnetic interference elimination, we developed a whole-body scanner that operates using a standard wall power outlet and without radiofrequency and magnetic shielding. We demonstrated its wide-ranging applicability for imaging various anatomical structures. Furthermore, we developed three-dimensional deep learning reconstruction to boost image quality by harnessing extensive high-field MRI data. These advances pave the way for affordable deep learning-powered ultra-low-field MRI scanners, addressing unmet clinical needs in diverse health care settings worldwide.


Subject(s)
Deep Learning , Magnetic Resonance Imaging , Whole Body Imaging , Magnetic Resonance Imaging/methods , Whole Body Imaging/methods , Humans , Imaging, Three-Dimensional/methods
2.
Sci Adv ; 9(38): eadi9327, 2023 09 22.
Article in English | MEDLINE | ID: mdl-37738341

ABSTRACT

In recent years, there has been an intensive development of portable ultralow-field magnetic resonance imaging (MRI) for low-cost, shielding-free, and point-of-care applications. However, its quality is poor and scan time is long. We propose a fast acquisition and deep learning reconstruction framework to accelerate brain MRI at 0.055 tesla. The acquisition consists of a single average three-dimensional (3D) encoding with 2D partial Fourier sampling, reducing the scan time of T1- and T2-weighted imaging protocols to 2.5 and 3.2 minutes, respectively. The 3D deep learning leverages the homogeneous brain anatomy available in high-field human brain data to enhance image quality, reduce artifacts and noise, and improve spatial resolution to synthetic 1.5-mm isotropic resolution. Our method successfully overcomes low-signal barrier, reconstructing fine anatomical structures that are reproducible within subjects and consistent across two protocols. It enables fast and quality whole-brain MRI at 0.055 tesla, with potential for widespread biomedical applications.


Subject(s)
Deep Learning , Humans , Brain/diagnostic imaging , Magnetic Resonance Imaging , Point-of-Care Systems
3.
Magn Reson Med ; 90(2): 400-416, 2023 08.
Article in English | MEDLINE | ID: mdl-37010491

ABSTRACT

PURPOSE: Recent development of ultra-low-field (ULF) MRI presents opportunities for low-power, shielding-free, and portable clinical applications at a fraction of the cost. However, its performance remains limited by poor image quality. Here, a computational approach is formulated to advance ULF MR brain imaging through deep learning of large-scale publicly available 3T brain data. METHODS: A dual-acquisition 3D superresolution model is developed for ULF brain MRI at 0.055 T. It consists of deep cross-scale feature extraction, attentional fusion of two acquisitions, and reconstruction. Models for T1 -weighted and T2 -weighted imaging were trained with 3D ULF image data sets synthesized from the high-resolution 3T brain data from the Human Connectome Project. They were applied to 0.055T brain MRI with two repetitions and isotropic 3-mm acquisition resolution in healthy volunteers, young and old, as well as patients. RESULTS: The proposed approach significantly enhanced image spatial resolution and suppressed noise/artifacts. It yielded high 3D image quality at 0.055 T for the two most common neuroimaging protocols with isotropic 1.5-mm synthetic resolution and total scan time under 20 min. Fine anatomical details were restored with intrasubject reproducibility, intercontrast consistency, and confirmed by 3T MRI. CONCLUSION: The proposed dual-acquisition 3D superresolution approach advances ULF MRI for quality brain imaging through deep learning of high-field brain data. Such strategy can empower ULF MRI for low-cost brain imaging, especially in point-of-care scenarios or/and in low-income and mid-income countries.


Subject(s)
Deep Learning , Humans , Reproducibility of Results , Magnetic Resonance Imaging/methods , Imaging, Three-Dimensional/methods , Neuroimaging/methods , Brain/diagnostic imaging
4.
Magn Reson Med ; 90(2): 502-519, 2023 08.
Article in English | MEDLINE | ID: mdl-37010506

ABSTRACT

PURPOSE: To develop a robust parallel imaging reconstruction method using spatial nulling maps (SNMs). METHODS: Parallel reconstruction using null operations (PRUNO) is a k-space reconstruction method where a k-space nulling system is derived using null-subspace bases of the calibration matrix. ESPIRiT reconstruction extends the PRUNO subspace concept by exploiting the linear relationship between signal-subspace bases and spatial coil sensitivity characteristics, yielding a hybrid-domain approach. Yet it requires empirical eigenvalue thresholding to mask the coil sensitivity information and is sensitive to signal- and null-subspace division. In this study, we combine the concepts of null-subspace PRUNO and hybrid-domain ESPIRiT to provide a more robust reconstruction method that extracts null-subspace bases of calibration matrix to calculate image-domain SNMs. Multi-channel images are reconstructed by solving an image-domain nulling system formed by SNMs that contain both coil sensitivity and finite image support information, therefore, circumventing the masking-related procedure. The proposed method was evaluated with multi-channel 2D brain and knee data and compared to ESPIRiT. RESULTS: The proposed hybrid-domain method produced quality reconstruction highly comparable to ESPIRiT with optimal manual masking. It involved no masking-related manual procedure and was tolerant of the actual division of null- and signal-subspace. Spatial regularization could be also readily incorporated to reduce noise amplification as in ESPIRiT. CONCLUSION: We provide an efficient hybrid-domain reconstruction method using multi-channel SNMs that are calculated from coil calibration data. It eliminates the need for coil sensitivity masking and is relatively insensitive to subspace separation, therefore, presenting a robust parallel imaging reconstruction procedure in practice.


Subject(s)
Algorithms , Magnetic Resonance Imaging , Magnetic Resonance Imaging/methods , Brain/diagnostic imaging , Calibration , Image Processing, Computer-Assisted/methods , Phantoms, Imaging
5.
Magn Reson Med ; 90(1): 280-294, 2023 07.
Article in English | MEDLINE | ID: mdl-37119514

ABSTRACT

PURPOSE: To develop a truly calibrationless reconstruction method that derives An Eigenvalue Approach to Autocalibrating Parallel MRI (ESPIRiT) maps from uniformly-undersampled multi-channel MR data by deep learning. METHODS: ESPIRiT, one commonly used parallel imaging reconstruction technique, forms the images from undersampled MR k-space data using ESPIRiT maps that effectively represents coil sensitivity information. Accurate ESPIRiT map estimation requires quality coil sensitivity calibration or autocalibration data. We present a U-Net based deep learning model to estimate the multi-channel ESPIRiT maps directly from uniformly-undersampled multi-channel multi-slice MR data. The model is trained using fully-sampled multi-slice axial brain datasets from the same MR receiving coil system. To utilize subject-coil geometric parameters available for each dataset, the training imposes a hybrid loss on ESPIRiT maps at the original locations as well as their corresponding locations within the standard reference multi-slice axial stack. The performance of the approach was evaluated using publicly available T1-weighed brain and cardiac data. RESULTS: The proposed model robustly predicted multi-channel ESPIRiT maps from uniformly-undersampled k-space data. They were highly comparable to the reference ESPIRiT maps directly computed from 24 consecutive central k-space lines. Further, they led to excellent ESPIRiT reconstruction performance even at high acceleration, exhibiting a similar level of errors and artifacts to that by using reference ESPIRiT maps. CONCLUSION: A new deep learning approach is developed to estimate ESPIRiT maps directly from uniformly-undersampled MR data. It presents a general strategy for calibrationless parallel imaging reconstruction through learning from the coil and protocol-specific data.


Subject(s)
Deep Learning , Image Processing, Computer-Assisted/methods , Algorithms , Magnetic Resonance Imaging/methods , Brain/diagnostic imaging
6.
IEEE Trans Med Imaging ; 42(6): 1644-1655, 2023 06.
Article in English | MEDLINE | ID: mdl-37018640

ABSTRACT

Low-rank technique has emerged as a powerful calibrationless alternative for parallel magnetic resonance (MR) imaging. Calibrationless low-rank reconstruction, such as low-rank modeling of local k-space neighborhoods (LORAKS), implicitly exploits both coil sensitivity modulations and the finite spatial support constraint of MR images through an iterative low-rank matrix recovery process. Although powerful, this slow iteration process is computationally demanding and reconstruction requires empirical rank optimization, hampering its robust applications for high-resolution volume imaging. This paper proposes a fast and calibrationless low-rank reconstruction of undersampled multi-slice MR brain data, based on the finite spatial support constraint reformulation with a direct deep learning estimation of spatial support maps. The iteration process of low-rank reconstruction is unrolled into a complex-valued network by training on fully-sampled multi-slice axial brain datasets acquired from the same MR coil system. To utilize coil-subject geometric parameters available for datasets, the model minimizes a hybrid loss on two sets of spatial support maps, corresponding to brain data at the original slice locations as actually acquired and nearby locations within the standard reference coordinate. This deep learning framework was integrated with LORAKS reconstruction and was evaluated with publically available gradient-echo T1-weighted brain datasets. It directly produced high-quality multi-channel spatial support maps from undersampled data, enabling rapid reconstruction without iteration. Moreover, it led to effective reductions of artifacts and noise amplification at high acceleration. In summary, our proposed deep learning framework offers a new strategy to advance the existing calibrationless low-rank reconstruction, rendering it computationally efficient, simple, and robust in practice.


Subject(s)
Deep Learning , Image Processing, Computer-Assisted , Image Processing, Computer-Assisted/methods , Algorithms , Magnetic Resonance Imaging/methods , Brain/diagnostic imaging
7.
Nat Commun ; 14(1): 2195, 2023 04 17.
Article in English | MEDLINE | ID: mdl-37069169

ABSTRACT

As a key oscillatory activity in the brain, thalamic spindle activities are long believed to support memory consolidation. However, their propagation characteristics and causal actions at systems level remain unclear. Using functional MRI (fMRI) and electrophysiology recordings in male rats, we found that optogenetically-evoked somatosensory thalamic spindle-like activities targeted numerous sensorimotor (cortex, thalamus, brainstem and basal ganglia) and non-sensorimotor limbic regions (cortex, amygdala, and hippocampus) in a stimulation frequency- and length-dependent manner. Thalamic stimulation at slow spindle frequency (8 Hz) and long spindle length (3 s) evoked the most robust brain-wide cross-modal activities. Behaviorally, evoking these global cross-modal activities during memory consolidation improved visual-somatosensory associative memory performance. More importantly, parallel visual fMRI experiments uncovered response potentiation in brain-wide sensorimotor and limbic integrative regions, especially superior colliculus, periaqueductal gray, and insular, retrosplenial and frontal cortices. Our study directly reveals that thalamic spindle activities propagate in a spatiotemporally specific manner and that they consolidate associative memory by strengthening multi-target memory representation.


Subject(s)
Memory Consolidation , Male , Rats , Animals , Memory Consolidation/physiology , Brain/diagnostic imaging , Thalamus/diagnostic imaging , Thalamus/physiology , Frontal Lobe/physiology , Magnetic Resonance Imaging
8.
Neuroimage ; 270: 119943, 2023 04 15.
Article in English | MEDLINE | ID: mdl-36828157

ABSTRACT

Despite its prominence in learning and memory, hippocampal influence in early auditory processing centers remains unknown. Here, we examined how hippocampal activity modulates sound-evoked responses in the auditory midbrain and thalamus using optogenetics and functional MRI (fMRI) in rodents. Ventral hippocampus (vHP) excitatory neuron stimulation at 5 Hz evoked robust hippocampal activity that propagates to the primary auditory cortex. We then tested 5 Hz vHP stimulation paired with either natural vocalizations or artificial/noise acoustic stimuli. vHP stimulation enhanced auditory responses to vocalizations (with a negative or positive valence) in the inferior colliculus, medial geniculate body, and auditory cortex, but not to their temporally reversed counterparts (artificial sounds) or broadband noise. Meanwhile, pharmacological vHP inactivation diminished response selectivity to vocalizations. These results directly reveal the large-scale hippocampal participation in natural sound processing at early centers of the ascending auditory pathway. They expand our present understanding of hippocampus in global auditory networks.


Subject(s)
Auditory Cortex , Inferior Colliculi , Inferior Colliculi/physiology , Auditory Pathways/physiology , Auditory Cortex/physiology , Acoustic Stimulation/methods , Auditory Perception/physiology , Geniculate Bodies/physiology , Hippocampus
9.
Sci Adv ; 8(46): eabo2098, 2022 Nov 18.
Article in English | MEDLINE | ID: mdl-36383661

ABSTRACT

Major depressive disorder (MDD) is a devastating mental disorder that affects up to 17% of the population worldwide. Although brain-wide network-level abnormalities in MDD patients via resting-state functional magnetic resonance imaging (rsfMRI) exist, the mechanisms underlying these network changes are unknown, despite their immense potential for depression diagnosis and management. Here, we show that the astrocytic calcium-deficient mice, inositol 1,4,5-trisphosphate-type-2 receptor knockout mice (Itpr2-/- mice), display abnormal rsfMRI functional connectivity (rsFC) in depression-related networks, especially decreased rsFC in medial prefrontal cortex (mPFC)-related pathways. We further uncover rsFC decreases in MDD patients highly consistent with those of Itpr2-/- mice, especially in mPFC-related pathways. Optogenetic activation of mPFC astrocytes partially enhances rsFC in depression-related networks in both Itpr2-/- and wild-type mice. Optogenetic activation of the mPFC neurons or mPFC-striatum pathway rescues disrupted rsFC and depressive-like behaviors in Itpr2-/- mice. Our results identify the previously unknown role of astrocyte dysfunction in driving rsFC abnormalities in depression.

10.
NMR Biomed ; 35(7): e4695, 2022 07.
Article in English | MEDLINE | ID: mdl-35032072

ABSTRACT

We propose a multi-slice acquisition with orthogonally alternating phase encoding (PE) direction and subsequent joint calibrationless reconstruction for accelerated multiple individual 2D slices or multi-slice 2D Cartesian MRI. Specifically, multi-slice multi-channel data are first acquired with random or uniform PE undersampling while orthogonally alternating PE direction between adjacent slices. They are then jointly reconstructed through a recently developed low-rank multi-slice Hankel tensor completion (MS-HTC) approach. The proposed acquisition and reconstruction strategy was evaluated with human brain MR data. It effectively suppressed aliasing artifacts even at high acceleration factor, outperforming the existing MS-HTC approach, where PE direction is the same between adjacent slices. More importantly, the new strategy worked robustly with uniform undersampling or random undersampling without any consecutive central k-space lines. In summary, our proposed multi-slice MRI strategy exploits both coil sensitivity and image content similarities across adjacent slices. Orthogonally alternating PE direction among slices substantially facilitates the low-rank completion process and improves image reconstruction quality. This new strategy is applicable to uniform and random PE undersampling. It can be easily implemented in practice for Cartesian parallel imaging of multiple individual 2D slices without any coil sensitivity calibration.


Subject(s)
Image Processing, Computer-Assisted , Magnetic Resonance Imaging , Algorithms , Artifacts , Brain/diagnostic imaging , Calibration , Humans , Image Processing, Computer-Assisted/methods , Magnetic Resonance Imaging/methods
11.
Magn Reson Med ; 87(2): 999-1014, 2022 02.
Article in English | MEDLINE | ID: mdl-34611904

ABSTRACT

PURPOSE: To provide a complex-valued deep learning approach for partial Fourier (PF) reconstruction of complex MR images. METHODS: Conventional PF reconstruction methods, such as projection onto convex sets (POCS), uses low-resolution image phase information from the central symmetrically sampled k-space for image reconstruction. However, this smooth phase constraint undermines the phase estimation accuracy in presence of rapid local phase variations, causing image artifacts and limiting the extent of PF reconstruction. Using both magnitude and phase characteristics in big complex image datasets, we propose a complex-valued deep learning approach with an unrolled network architecture for PF reconstruction that iteratively reconstructs PF sampled data and enforces data consistency. We evaluate our approach for reconstructing both spin-echo and gradient-echo data. RESULTS: The proposed method outperformed the iterative POCS PF reconstruction method. It produced better artifact suppression and recovery of both image magnitude and phase details in presence of local phase changes. No noise amplification was observed even for highly PF reconstruction. Moreover, the network trained on axial brain data could reconstruct sagittal and coronal brain and knee data. This method could be extended to 2D PF reconstruction and joint multi-slice PF reconstruction. CONCLUSION: Our proposed method can effectively reconstruct MR data even at low PF fractions, yielding high-fidelity magnitude and phase images. It presents a valuable alternative to conventional PF reconstruction, especially for phase-sensitive 2D or 3D MRI applications.


Subject(s)
Image Processing, Computer-Assisted , Phase Variation , Algorithms , Humans , Magnetic Resonance Imaging , Neural Networks, Computer
12.
Nat Commun ; 12(1): 7238, 2021 12 14.
Article in English | MEDLINE | ID: mdl-34907181

ABSTRACT

Magnetic resonance imaging is a key diagnostic tool in modern healthcare, yet it can be cost-prohibitive given the high installation, maintenance and operation costs of the machinery. There are approximately seven scanners per million inhabitants and over 90% are concentrated in high-income countries. We describe an ultra-low-field brain MRI scanner that operates using a standard AC power outlet and is low cost to build. Using a permanent 0.055 Tesla Samarium-cobalt magnet and deep learning for cancellation of electromagnetic interference, it requires neither magnetic nor radiofrequency shielding cages. The scanner is compact, mobile, and acoustically quiet during scanning. We implement four standard clinical neuroimaging protocols (T1- and T2-weighted, fluid-attenuated inversion recovery like, and diffusion-weighted imaging) on this system, and demonstrate preliminary feasibility in diagnosing brain tumor and stroke. Such technology has the potential to meet clinical needs at point of care or in low and middle income countries.


Subject(s)
Magnetic Resonance Imaging/instrumentation , Neuroimaging/instrumentation , Adult , Brain Neoplasms/diagnostic imaging , Deep Learning , Diffusion Magnetic Resonance Imaging , Equipment Design , Feasibility Studies , Humans , Magnetic Fields , Magnetic Resonance Imaging/economics , Magnets , Neuroimaging/economics , Phantoms, Imaging , Point-of-Care Systems , Stroke/diagnostic imaging
13.
Neuroimage ; 235: 118032, 2021 07 15.
Article in English | MEDLINE | ID: mdl-33836268

ABSTRACT

Brain possesses a complex spatiotemporal architecture for efficient information processing and computing. However, it remains unknown how neural signal propagates to its intended targets brain-wide. Using optogenetics and functional MRI, we arbitrarily initiated various discrete neural activity pulse trains with different temporal patterns and revealed their distinct long-range propagation targets within the well-defined, topographically organized somatosensory thalamo-cortical circuit. We further observed that such neural activity propagation over long range could modulate brain-wide sensory functions. Electrophysiological analysis indicated that distinct propagation pathways arose from system level neural adaptation and facilitation in response to the neural activity temporal characteristics. Together, our findings provide fundamental insights into the long-range information transfer and processing. They directly support that temporal coding underpins the whole brain functional architecture in presence of the vast and relatively static anatomical architecture.


Subject(s)
Brain/physiology , Neural Pathways/physiology , Animals , Brain Mapping , Magnetic Resonance Imaging , Male , Nerve Net/physiology , Optogenetics , Rats , Rats, Sprague-Dawley , Somatosensory Cortex/physiology , Thalamus/physiology
14.
Magn Reson Med ; 85(6): 3256-3271, 2021 06.
Article in English | MEDLINE | ID: mdl-33533092

ABSTRACT

PURPOSE: To jointly reconstruct highly undersampled multicontrast two-dimensional (2D) datasets through a low-rank Hankel tensor completion framework. METHODS: A multicontrast Hankel tensor completion (MC-HTC) framework is proposed to exploit the shareable information in multicontrast datasets with respect to their highly correlated image structure, common spatial support, and shared coil sensitivity for joint reconstruction. This is achieved by first organizing multicontrast k-space datasets into a single block-wise Hankel tensor. Subsequent low-rank tensor approximation via higher-order singular value decomposition (HOSVD) uses the image structural correlation by considering different contrasts as virtual channels. Meanwhile, the HOSVD imposes common spatial support and shared coil sensitivity by treating data from different contrasts as from additional k-space kernels. The missing k-space data are then recovered by iteratively performing such low-rank approximation and enforcing data consistency. This joint reconstruction framework was evaluated using multicontrast multichannel 2D human brain datasets (T1 -weighted, T2 -weighted, fluid-attenuated inversion recovery, and T1 -weighted-inversion recovery) of identical image geometry with random and uniform undersampling schemes. RESULTS: The proposed method offered high acceleration, exhibiting significantly less residual errors when compared with both single-contrast SAKE (simultaneous autocalibrating and k-space estimation) and multicontrast J-LORAKS (joint parallel-imaging-low-rank matrix modeling of local k-space neighborhoods) low-rank reconstruction. Furthermore, the MC-HTC framework was applied uniquely to Cartesian uniform undersampling by incorporating a novel complementary k-space sampling strategy where the phase-encoding direction among different contrasts is orthogonally alternated. CONCLUSION: The proposed MC-HTC approach presents an effective tensor completion framework to jointly reconstruct highly undersampled multicontrast 2D datasets without coil-sensitivity calibration.


Subject(s)
Algorithms , Magnetic Resonance Imaging , Brain/diagnostic imaging , Calibration , Contrast Media , Humans , Image Processing, Computer-Assisted
15.
Magn Reson Med ; 85(2): 897-911, 2021 02.
Article in English | MEDLINE | ID: mdl-32966651

ABSTRACT

PURPOSE: To provide joint calibrationless parallel imaging reconstruction of highly accelerated multislice 2D MR k-space data. METHODS: Adjacent image slices in multislice MR data have similar coil sensitivity maps, spatial support, and image content. Such similarities can be utilized to improve image quality by reconstructing multiple slices jointly with low-rank tensor completion. Specifically, the multichannel k-space data from multiple slices are constructed into a block-wise Hankel tensor and iteratively updated by promoting tensor low-rankness through higher-order SVD. This multislice block-wise Hankel tensor completion was implemented for 2D spiral and Cartesian k-space undersampling where sampling patterns vary between adjacent slices. The approach was evaluated with human brain MR data and compared to the traditional single-slice simultaneous autocalibrating and k-space estimation reconstruction. RESULTS: The proposed multislice block-wise Hankel tensor completion approach robustly reconstructed highly undersampled multislice 2D spiral and Cartesian data. It produced substantially lower level of artifacts compared to the traditional single-slice simultaneous autocalibrating and k-space estimation reconstruction. Quantitative evaluation using error maps and root mean square error demonstrated its significantly improved performance in terms of residual artifacts and root mean square error. CONCLUSION: Our proposed multislice block-wise Hankel tensor completion method exploits the similar coil sensitivity and image content within multislice MR data through a tensor completion framework. It offers a new and effective approach to acquire and reconstruct highly undersampled multislice MR data in a calibrationless manner.


Subject(s)
Algorithms , Image Processing, Computer-Assisted , Artifacts , Brain/diagnostic imaging , Humans , Magnetic Resonance Imaging , Phantoms, Imaging
16.
Annu Int Conf IEEE Eng Med Biol Soc ; 2020: 1100-1103, 2020 07.
Article in English | MEDLINE | ID: mdl-33018178

ABSTRACT

Alzheimer's disease (AD) is a degenerative brain disease and the most common cause of dementia. Early stage ß-amyloid oligomers (AßOs) and late stage Aß plaques are the pathological hallmarks of AD brains. AßOs are known to be more neurotoxic and contribute to neuronal damage. Most current approaches are focused on detecting Aß plaques, which occurs at the late stage of AD, and are limited by poor sensitivity and/or contrast agent toxicity. In previous studies, we developed a new curcumin-conjugated magnetic nanoparticle (Cur-MNPs) to target the Aß pathologies. In this study, we investigate the in vivo feasibility of this novel Cur-MNPs to detect Aß pathologies at the early and late stages of AD in transgenic AD mice and perform immunohistochemical examinations to validate the specific targeting of various form of Aß pathologies.


Subject(s)
Alzheimer Disease , Alzheimer Disease/diagnosis , Amyloid beta-Peptides , Animals , Early Diagnosis , Magnetic Resonance Imaging , Mice , Plaque, Amyloid/diagnostic imaging
17.
Neuroimage ; 201: 115985, 2019 11 01.
Article in English | MEDLINE | ID: mdl-31299370

ABSTRACT

Blood-oxygen-level-dependent (BOLD) resting-state functional MRI (rsfMRI) has emerged as a valuable tool to map complex brain-wide functional networks, predict cognitive performance and identify biomarkers for neurological diseases. However, interpreting these findings poses challenges, as the neural basis of rsfMRI connectivity remains poorly understood. The thalamus serves as a relay station and modulates diverse long-range cortical functional integrations, yet few studies directly interrogate its role in brain-wide rsfMRI connectivity. Utilizing a multi-modal approach of rsfMRI, optogenetic stimulation and multi-depth cortical electrophysiology recording, we examined whether and how the somatosensory thalamus contributes to cortical interhemispheric rsfMRI connectivity. We found that low frequency (1 Hz) optogenetic stimulation of somatosensory-specific ventral posteromedial (VPM) thalamocortical excitatory neurons increased the interhemispheric rsfMRI connectivity in all examined sensory cortices, somatosensory, visual and auditory, and the local intrahemispheric BOLD activity at infraslow frequency (0.01-0.1 Hz). In parallel, multi-depth local field potential recordings at bilateral primary somatosensory cortices revealed increased interhemispheric correlations of low frequency neural oscillations (i.e., mainly < 10 Hz) at all cortical layers. Meanwhile, pharmacologically inhibiting VPM thalamocortical neurons decreased interhemispheric rsfMRI connectivity and local intrahemispheric infraslow BOLD activity in all sensory cortices. Taken together, our findings demonstrate that low frequency activities in the thalamo-cortical network contribute to brain-wide rsfMRI connectivity, highlighting the thalamus as a pivotal region that underlies rsfMRI connectivity.


Subject(s)
Neural Pathways/physiology , Sensory Receptor Cells/physiology , Thalamus/physiology , Animals , Brain Mapping/methods , Magnetic Resonance Imaging , Male , Rats , Rats, Sprague-Dawley , Rest
18.
Proc Natl Acad Sci U S A ; 116(20): 10122-10129, 2019 05 14.
Article in English | MEDLINE | ID: mdl-31028140

ABSTRACT

Blood oxygen level-dependent functional MRI (fMRI) constitutes a powerful neuroimaging technology to map brain-wide functions in response to specific sensory or cognitive tasks. However, fMRI mapping of the vestibular system, which is pivotal for our sense of balance, poses significant challenges. Physical constraints limit a subject's ability to perform motion- and balance-related tasks inside the scanner, and current stimulation techniques within the scanner are nonspecific to delineate complex vestibular nucleus (VN) pathways. Using fMRI, we examined brain-wide neural activity patterns elicited by optogenetically stimulating excitatory neurons of a major vestibular nucleus, the ipsilateral medial VN (MVN). We demonstrated robust optogenetically evoked fMRI activations bilaterally at sensorimotor cortices and their associated thalamic nuclei (auditory, visual, somatosensory, and motor), high-order cortices (cingulate, retrosplenial, temporal association, and parietal), and hippocampal formations (dentate gyrus, entorhinal cortex, and subiculum). We then examined the modulatory effects of the vestibular system on sensory processing using auditory and visual stimulation in combination with optogenetic excitation of the MVN. We found enhanced responses to sound in the auditory cortex, thalamus, and inferior colliculus ipsilateral to the stimulated MVN. In the visual pathway, we observed enhanced responses to visual stimuli in the ipsilateral visual cortex, thalamus, and contralateral superior colliculus. Taken together, our imaging findings reveal multiple brain-wide central vestibular pathways. We demonstrate large-scale modulatory effects of the vestibular system on sensory processing.


Subject(s)
Brain Mapping , Vestibular Nuclei/physiology , Animals , Auditory Perception/physiology , Magnetic Resonance Imaging , Male , Optogenetics , Rats, Sprague-Dawley , Visual Perception/physiology
19.
Magn Reson Med ; 81(3): 1924-1934, 2019 03.
Article in English | MEDLINE | ID: mdl-30368895

ABSTRACT

PURPOSE: To provide simultaneous multislice (SMS) EPI reconstruction with k-space implementation and robust Nyquist ghost correction. METHODS: 2D phase error correction SENSE (PEC-SENSE) was recently developed for Nyquist ghost correction in SMS EPI reconstruction for which virtual coil simultaneous autocalibration and k-space estimation (VC-SAKE) was used to remove slice-dependent Nyquist ghosts and intershot 2D phase variations in multi-shot EPI reference scan. However, masking coil sensitivity maps to exclude background region in PEC-SENSE and manually selecting slice-wise target ranks in VC-SAKE are cumbersome procedures in practice. To avoid masking, the concept of PEC-SENSE is extended to k-space implementation and termed as PEC-GRAPPA. Furthermore, a singular value shrinkage scheme is incorporated in VC-SAKE to circumvent the empirical slice-wise target rank selection. PEC-GRAPPA was evaluated and compared to PEC-SENSE with/without masking and 1D linear phase correction GRAPPA. RESULTS: PEC-GRAPPA robustly reconstructed SMS EPI images from 7T phantom and human brain data, effectively removing the phase error-induced artifacts. The resulting residual artifact level and temporal SNR were comparable to those by PEC-SENSE with careful tuning. PEC-GRAPPA outperformed PEC-SENSE without masking and 1D linear phase correction GRAPPA. CONCLUSION: Our proposed PEC-GRAPPA approach effectively removes the artifacts caused by Nyquist ghosts in SMS EPI without cumbersome tuning. This approach provides a robust and practical implementation of SMS EPI reconstruction in k-space with slice-dependent 2D Nyquist ghost correction.


Subject(s)
Brain/diagnostic imaging , Echo-Planar Imaging , Image Enhancement/methods , Algorithms , Artifacts , Calibration , Healthy Volunteers , Humans , Image Processing, Computer-Assisted , Phantoms, Imaging , Reference Values , Signal Processing, Computer-Assisted , Signal-To-Noise Ratio , Time Factors
20.
Annu Int Conf IEEE Eng Med Biol Soc ; 2018: 5527-5530, 2018 Jul.
Article in English | MEDLINE | ID: mdl-30441589

ABSTRACT

The brain integrates information from different sensory modalities to form a representation of the environment and facilitate behavioral responses. The auditory midbrain or inferior colliculus (IC) is a pivotal station in the auditory system, integrating ascending and descending information from various auditory sources and cortical systems. The present study investigated the modulation of auditory responses in the IC by visual stimuli of different frequencies and intensities in rats using functional MRI (fMRI). Low-frequency (1 Hz) high-intensity visual stimulus suppressed IC auditory responses. However, high-frequency (10 Hz) or low-intensity visual stimuli did not alter the IC auditory responses. This finding demonstrates that cross-modal processing occurs in the IC in a manner that depends on the stimulus. Furthermore, only low-frequency high-intensity visual stimulus elicited responses in non-visual cortical regions, suggesting that the above cross-modal modulation effect may arise from top-down cortical feedback. These fMRI results provide insight to guide future studies of cross-modal processing in sensory pathways.


Subject(s)
Inferior Colliculi , Magnetic Resonance Imaging , Acoustic Stimulation , Animals , Auditory Pathways , Auditory Perception , Brain Mapping , Mesencephalon , Rats
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