Large scale data acquisition of simultaneous MRI and speech

We describe an arrangement for simultaneous recording of speech and vocal tract geometry in patients undergoing surgery involving this area. Experimental design is considered from an articulatory phonetic point of view. The speech signals are recorded with an acoustic-electrical arrangement. The vocal tract is simultaneously imaged with MRI. A MATLAB-based system controls the timing of speech recording and MR image acquisition. The speech signals are cleaned from acoustic MRI noise by an adaptive signal processing algorithm. Finally, a vowel data set from pilot experiments is qualitatively compared both with validation data from the anechoic chamber and with Helmholtz resonances of the vocal tract volume, obtained using FEM.     

Developments in active noise control sound systems for magnetic resonance imaging

Magnetic resonance imaging (MRI) scanners can produce noise measuring over 130 dB SPL. This noise stimulates the auditory nervous system, limiting the dynamic range for stimulus driven activity in functional MRI (fMRI) experiments and can influence other brain functions. Even for structural scans it causes subject anxiety and discomfort in addition to the impediment to communications. Here we describe the realization and validation of a sound system for sound presentation inside an MRI scanner and the modifications to a standard active noise control technique for use in the noisy and compact environment of the scanner. This paper provides a review of the technology available for the presentation of audio stimuli in an MRI environment and the modifications required for the active control of scanner noise. Some of the content has been previously published [Chambers J, Akeroyd MA, Summerfield AQ, Palmer AR. Active control of the volume acquisition noise in functional magnetic resonance imaging: method and psychoacoustical evaluation. J Acoust Soc Am 2001;110(6):3041-54; Levitt H. Transformed up-down methods in psychoacoustics. J Acoust Soc Am 1971;49:467-77], but this paper goes further in describing the stages of development as the system performance was optimised. The performance of the system and both the objective and subjective reduction of the scanner noise are reported. Finally, we discuss recent improvements to the system that are currently being evaluated and describe the theory of opto-acoustical transducers that operate on the principle of light modulation. These are immune from, and do not create, electro-magnetic interference (EMI) and radio-frequency interference (RFI).     

An approach to real-time magnetic resonance imaging for speech production

Magnetic resonance imaging (MRI) has served as a valuable tool for studying static postures in speech production. Now, recent improvements in temporal resolution are making it possible to examine the dynamics of vocal-tract shaping during fluent speech using MRI. The present study uses spiral k-space acquisitions with a low flip-angle gradient echo pulse sequence on a conventional GE Signa 1.5-T CV/i scanner. This strategy allows for acquisition rates of 8-9 images per second and reconstruction rates of 20-24 images per second, making veridical movies of speech production now possible. Segmental durations, positions, and interarticulator timing can all be quantitatively evaluated. Data show clear real-time movements of the lips, tongue, and velum. Sample movies and data analysis strategies are presented.     

MRISim:磁共振成像仿真实验软件包

本文基于数值计算模拟技术,开发了模拟磁共振成像（MRI）数据采集与图像重建的仿真软件包——MRISim.虚拟数据采集部分通过对设备硬件、样品（标样或人体部位）进行物理数学建模后,构建原始模拟信号,并填充k空间,然后再基于k空间数据实现磁共振图像重建.该软件可以通过参数的任意调节对影响磁共振图像质量的因素进行可视化分析,包括11种常见伪影的特征和成因分析.我们的研究表明应用该仿真软件可以弥补台式MRI扫描仪价格昂贵、实验时间长等不足之处,实现对相关科技人员的批量化、规模化的实践操作培训.     

Autonomous magnetic resonance imaging

Access to Magnetic Resonance Imaging (MRI) across developing countries ranges from being prohibitive to scarcely available. For example, eleven countries in Africa have no scanners. One critical limitation is the absence of skilled manpower required for MRI usage. Some of these challenges can be mitigated using autonomous MRI (AMRI) operation. In this work, we demonstrate AMRI to simplify MRI workflow by separating the required intelligence and user interaction from the acquisition hardware. AMRI consists of three components: user node, cloud and scanner. The user node voice interacts with the user and presents the image reconstructions at the end of the AMRI exam. The cloud generates pulse sequences and performs image reconstructions while the scanner acquires the raw data. An AMRI exam is a custom brain screen protocol comprising of one T₁-, T₂- and T₂*-weighted exams. A neural network is trained to incorporate Intelligent Slice Planning (ISP) at the start of the AMRI exam. A Look Up Table was designed to perform intelligent protocolling by optimizing for contrast value while satisfying signal to noise ratio and acquisition time constraints. Data were acquired from four healthy volunteers for three experiments with different acquisition time constraints to demonstrate standard and self-administered AMRI. The source code is available online. AMRI achieved an average SNR of 22.86 ± 0.89 dB across all experiments with similar contrast. Experiment #3 (33.66% shorter table time than experiment #1) yielded a SNR of 21.84 ± 6.36 dB compared to 23.48 ± 7.95 dB for experiment #1. AMRI can potentially enable multiple scenarios to facilitate rapid prototyping and research and streamline radiological workflow. We believe we have demonstrated the first Autonomous MRI of the brain.     

Undersampled MRI reconstruction with patch-based directional wavelets

Compressed sensing has shown great potential in reducing data acquisition time in magnetic resonance imaging (MRI). In traditional compressed sensing MRI methods, an image is reconstructed by enforcing its sparse representation with respect to a preconstructed basis or dictionary. In this paper, patch-based directional wavelets are proposed to reconstruct images from undersampled k-space data. A parameter of patch-based directional wavelets, indicating the geometric direction of each patch, is trained from the reconstructed image using conventional compressed sensing MRI methods and incorporated into the sparsifying transform to provide the sparse representation for the image to be reconstructed. A reconstruction formulation is proposed and solved via an efficient alternating direction algorithm. Simulation results on phantom and in vivo data indicate that the proposed method outperforms conventional compressed sensing MRI methods in preserving the edges and suppressing the noise. Besides, the proposed method is not sensitive to the initial image when training directions.     

Whole volume brain extraction for multi-centre,multi-disease FLAIR MRI datasets

Automatic segmentation of the brain from magnetic resonance images (MRI) is a fundamental step in many neuroimaging processing frameworks. There are mature technologies for this task for T1- and T2-weighted MRI; however, a widely-accepted brain extraction method for Fluid-Attenuated Inversion Recovery (FLAIR) MRI has yet to be established. FLAIR MRI are becoming increasingly important for the analysis of neurodegenerative diseases and tools developed for this sequence would have clinical value. To maximize translation opportunities and for large scale research studies, algorithms for brain extraction in FLAIR MRI should generalize to multi-centre (MC) data. To this end, this work proposes a fully automated, whole volume brain extraction methodology for MC FLAIR MRI datasets. The framework is built using a novel standardization framework which reduces acquisition artifacts, standardizes the intensities of tissues and normalizes the spatial coordinates of brain tissue across MC datasets. Using the standardized datasets, an intuitive set of features based on intensity, spatial location and gradients are extracted and classified using a random forest (RF) classifier to segment the brain tissue class. A series of experiments were conducted to optimize classifier parameters, and to determine segmentation accuracy for standardized and unstandardized (original) data, as a function of scanner vendor, feature type and disease type. The models are trained, tested and validated on 156 image volumes (∼8000 image slices) from two multi-centre, multi-disease datasets, acquired with varying imaging parameters from 30 centres and three scanner vendors. The image datasets, denoted as CAIN and ADNI for vascular and dementia disease, respectively, represent a diverse collection of MC data to test the generalization capabilities of the proposed design. Results demonstrate the importance of standardization for segmentation of MC data, as models trained on standardized data yielded a drastic improvement in brain extraction accuracy compared to the original, unstandardized data (CAIN: DSC = 91% and ADNI: DSC = 86% vs. CAIN: 78% and ADNI: 65%). It was also found that models created from one scanner vendor based on unstandardized data yielded poor segmentation results in data acquired from other scanner vendors, which was improved through standardization. These results demonstrate that to create consistency in segmentations from multi-institutional datasets it is paramount that MC variability be mitigated to improve stability and to ensure generalization of machine learning algorithms for MRI.     

Low-field magnetic resonance imaging using multiplicative regularization

In this paper we present a magnetic resonance imaging (MRI) technique that is based on multiplicative regularization. Instead of adding a regularizing objective function to a data fidelity term, we multiply by such a regularizing function. By following this approach, no regularization parameter needs to be determined for each new data set that is acquired. Reconstructions are obtained by iteratively updating the images using short-term conjugate gradient-type update formulas and Polak-Ribière update directions. We show that the algorithm can be used as an image reconstruction algorithm and as a denoising algorithm. We illustrate the performance of the algorithm on two-dimensional simulated low-field MR data that is corrupted by noise and on three-dimensional measured data obtained from a low-field MR scanner. Our reconstruction results show that the algorithm effectively suppresses noise and produces accurate reconstructions even for low-field MR signals with a low signal-to-noise ratio.     

Generalized total variation-based MRI Rician denoising model with spatially adaptive regularization parameters

Magnetic resonance imaging (MRI) is an outstanding medical imaging modality but the quality often suffers from noise pollution during image acquisition and transmission. The purpose of this study is to enhance image quality using feature-preserving denoising method. In current literature, most existing MRI denoising methods did not simultaneously take the global image prior and local image features into account. The denoising method proposed in this paper is implemented based on an assumption of spatially varying Rician noise map. A two-step wavelet-domain estimation method is developed to extract the noise map. Following a Bayesian modeling approach, a generalized total variation-based MRI denoising model is proposed based on global hyper-Laplacian prior and Rician noise assumption. The proposed model has the properties of backward diffusion in local normal directions and forward diffusion in local tangent directions. To further improve the denoising performance, a local variance estimator-based method is introduced to calculate the spatially adaptive regularization parameters related to local image features and spatially varying noise map. The main benefit of the proposed method is that it takes full advantage of the global MR image prior and local image features. Numerous experiments have been conducted on both synthetic and real MR data sets to compare our proposed model with some state-of-the-art denoising methods. The experimental results have demonstrated the superior performance of our proposed model in terms of quantitative and qualitative image quality evaluations.     

Prediction method for listening score and psychological impression taking into account hearing loss due to factors such as aging

This paper considers how the listening scores obtained for audio signals and psychological impressions for speech audibility change when factors such as hearing loss due to aging are taken into account. Concretely, frequency filters for simulating hearing loss due to factors such as aging are first prepared. Next, psychological listening experiments are conducted in which both the audio signal and the noise passing through the above-mentioned filters are transmitted to subjects with normal hearing. Using the observed experimental data, the relationships between the weighted-mean spectral distance and the listening scores of the audio signals and psychological impressions with respect to speech audibility are investigated. Next, based on these relationships, problems associated with the prediction of listening scores of audio signals and psychological impressions with respect to speech audibility are discussed. The predicted results are in good agreement with the observed values.     

Binaural speech unmasking and localization in noise with bilateral cochlear implants using envelope and fine-timing based strategies

Four adult bilateral cochlear implant users, with good open-set sentence recognition, were tested with three different sound coding strategies for binaural speech unmasking and their ability to localize 100 and 500 Hz click trains in noise. Two of the strategies tested were envelope-based strategies that are clinically widely used. The third was a research strategy that additionally preserved fine-timing cues at low frequencies. Speech reception thresholds were determined in diotic noise for diotic and interaurally time-delayed speech using direct audio input to a bilateral research processor. Localization in noise was assessed in the free field. Overall results, for both speech and localization tests, were similar with all three strategies. None provided a binaural speech unmasking advantage due to the application of 700 micros interaural time delay to the speech signal, and localization results showed similar response patterns across strategies that were well accounted for by the use of broadband interaural level cues. The data from both experiments combined indicate that, in contrast to normal hearing, timing cues available from natural head-width delays do not offer binaural advantages with present methods of electrical stimulation, even when fine-timing cues are explicitly coded.     

Audio-visual enhancement of speech in noise.

A key problem for telecommunication or human-machine communication systems concerns speech enhancement in noise. In this domain, a certain number of techniques exist, all of them based on an acoustic-only approach--that is, the processing of the audio corrupted signal using audio information (from the corrupted signal only or additive audio information). In this paper, an audio-visual approach to the problem is considered, since it has been demonstrated in several studies that viewing the speaker's face improves message intelligibility, especially in noisy environments. A speech enhancement prototype system that takes advantage of visual inputs is developed. A filtering process approach is proposed that uses enhancement filters estimated with the help of lip shape information. The estimation process is based on linear regression or simple neural networks using a training corpus. A set of experiments assessed by Gaussian classification and perceptual tests demonstrates that it is indeed possible to enhance simple stimuli (vowel-plosive-vowel sequences) embedded in white Gaussian noise.     

Optimizing Image Reconstruction in SENSE Using GPU

Parallel magnetic resonance imaging (MRI) (pMRI) uses multiple receiver coils to reduce the MRI scan time. To accelerate the data acquisition process in MRI, less amount of data is acquired from the scanner which leads to artifacts in the reconstructed images. SENSitivity Encoding (SENSE) is a reconstruction algorithm in pMRI to remove aliasing artifacts from the undersampled multi coil data and recovers fully sampled images. The main limitation of SENSE is computing inverse of the encoding matrix. This work proposes the inversion of encoding matrix using Jacobi singular value decomposition (SVD) algorithm for image reconstruction on GPUs to accelerate the reconstruction process. The performance of Jacobi SVD is compared with Gauss–Jordan algorithm. The simulations are performed on two datasets (brain and cardiac) with acceleration factors 2, 4, 6 and 8. The results show that the graphics processing unit (GPU) provides a speed up to 21.6 times as compared to CPU reconstruction. Jacobi SVD algorithm performs better in terms of acceleration in reconstructions on GPUs as compared to Gauss–Jordan method. The proposed algorithm is suitable for any number of coils and acceleration factors for SENSE reconstruction on real time processing systems.     

In-vivo diffusion MRI protocol optimization for the chimpanzee brain and examination of aging effects on the primate optic nerve at 3T

BackgroundDiffusion MRI (dMRI) data acquisition protocols are well-established on modern high-field clinical scanners for human studies. However, these protocols are not suitable for the chimpanzee (or other large-brained mammals) because of its substantial difference in head geometry and brain volume compared with humans. Therefore, an optimal dMRI data acquisition protocol dedicated to chimpanzee neuroimaging is needed.MethodsA multi-shot (4 segments) double spin-echo echo-planar imaging (MS-EPI) sequence and a single-shot double spin-echo EPI (SS-EPI) sequence were optimized separately for in vivo dMRI data acquisition of chimpanzees using a clinical 3T scanner. Correction for severe susceptibility-induced image distortion and signal drop-off of the chimpanzee brain was performed and evaluated using FSL software. DTI indices in different brain regions and probabilistic tractography were compared. A separate DTI data set from n=34 chimpanzees (13 to 56 years old) was collected using the optimal protocol. Age-related changes in diffusivity indices of optic nerve fibers were evaluated.ResultsThe SS-EPI sequence acquired dMRI data of the chimpanzee brain with approximately doubled the SNR as the MS-EPI sequence given the same scan time. The quality of white matter fiber tracking from the SS-EPI data was much higher than that from MS-EPI data. However, quantitative analysis of DTI indices showed no difference in most ROIs between the SS-EPI and MS-EPI sequences. The progressive evolution of diffusivity indices of optic nerves indicated mild changes in fiber bundles of chimpanzees aged 40 years and above.ConclusionThe single-shot EPI-based acquisition protocol provided better image quality of dMRI for chimpanzee brains and is recommended for in vivo dMRI study or clinical diagnosis of chimpanzees (or other large animals) using a clinical scanner. Also, the tendency of FA decrease or diffusivity increase in the optic nerve of aged chimpanzees was seen but did not show significant age-related changes, suggesting aging may have less impact on optic nerve fiber integrity of chimpanzees, in contrast to previous results for both macaque monkeys and humans.     

Interference from audio distracters during speechreading

Although many audio-visual speech experiments have focused on situations where the presence of an incongruent visual speech signal influences the perceived utterance heard by an observer, there are also documented examples of a related effect in which the presence of an incongruent audio speech signal influences the perceived utterance seen by an observer. This study examined the effects that different distracting audio signals had on performance in a color and number keyword speechreading task. When the distracting sound was noise, time-reversed speech, or continuous speech, it had no effect on speechreading. However, when the distracting audio signal consisted of speech that started at the same time as the visual stimulus, speechreading performance was substantially degraded. This degradation did not depend on the semantic similarity between the target and masker speech, but it was substantially reduced when the onset of the audio speech was shifted relative to that of the visual stimulus. Overall, these results suggest that visual speech perception is impaired by the presence of a simultaneous mismatched audio speech signal, but that other types of audio distracters have little effect on speechreading performance.     

Structural health monitoring by extraction of coherent guided waves from diffuse fields

This letter points out that, although in the audio signal domain low-pass filtering has been used to prevent aliasing noise from entering the baseband of speech signals, an antialias process in the speech feature domain is still needed to prevent high modulation frequency components from entering the baseband of speech features. The existence of aliasing noise in speech features is revealed via spectral analysis of speech feature streams. A method for suppressing such aliasing noise is proposed. Experiments on large vocabulary speech recognition show that antialias processing of speech features can improve speech recognition, especially for noisy speech.     

Resolution enhancement in MRI

We consider the problem of super-resolution reconstruction (SRR) in MRI. Subpixel-shifted MR images were taken in several fields of view (FOVs) to reconstruct a high-resolution image. A novel algorithm is presented. The algorithm can be applied locally and guarantees perfect reconstruction in the absence of noise. Results that demonstrate resolution improvement are given for phantom studies (mathematical model) as well as for MRI studies of a phantom carried out with a GE clinical scanner. The method raises questions that are discussed in the last section of the paper. Open questions should be answered in order to apply this method for clinical purposes.     

静音掩蔽和频域分段的音频指纹检索算法

为解决背景音及噪音等条件下音频检索识别率低的问题,提出静音掩蔽和频域分段的音频指纹检索算法。首先采用端点检测技术进行语音预处理,将有效语音帧重新组合并利用相邻子带能量差对其提取指纹特征,可有效解决静音帧指纹特征不鲁棒的问题。然后在检索匹配时根据不同音频信号在频域范围内的分布特点,对音频指纹在不同频率区间进行分段和加权,以更精确地计算模板和待检音频之间的相似度。实验表明,与Philips基线算法相比,所提算法在检索速度上提升了一倍,在受背景音等干扰的数据集上,平均准确率与召回率分别绝对提升17.94%和4.66%;与最新Philips算法相比,平均准确率与召回率分别绝对提升13.68%和2.45%。      

An advanced fully 3D OSEM reconstruction for positron emission tomography

A fully 3D OSEM reconstruction method for positron emission tomography (PET) based on sym-metries and sparse matrix technique is described. Great savings in both storage space and computation time were achieved by exploiting the symmetries of scanner and sparseness of the system matrix. More reduction of storage requirement was obtained by introducing the approximation of system matrix. Iteration-filter was per-formed to restrict image noise in reconstruction. Performances of simulation data and phantom data got from Micro-PET (Type: Epuls-166) demonstrated that similar image quality was achieved using the approximation of the system matrix.     

Adaptive fixed-point iterative shrinkage/thresholding algorithm for MR imaging reconstruction using compressed sensing

Recently compressed sensing (CS) has been applied to under-sampling MR image reconstruction for significantly reducing signal acquisition time. To guarantee the accuracy and efficiency of the CS-based MR image reconstruction, it necessitates determining several regularization and algorithm-introduced parameters properly in practical implementations. The regularization parameter is used to control the trade-off between the sparsity of MR image and the fidelity measures of k-space data, and thus has an important effect on the reconstructed image quality. The algorithm-introduced parameters determine the global convergence rate of the algorithm itself. These parameters make CS-based MR image reconstruction a more difficult scheme than traditional Fourier-based method while implemented on a clinical MR scanner. In this paper, we propose a new approach that reveals that the regularization parameter can be taken as a threshold in a fixed-point iterative shrinkage/thresholding algorithm (FPIST) and chosen by employing minimax threshold selection method. No extra parameter is introduced by FPIST. The simulation results on synthetic and real complex-valued MRI data show that the proposed method can adaptively choose the regularization parameter and effectively achieve high reconstruction quality. The proposed method should prove very useful for practical CS-based MRI applications.