Monte Carlo-based Noise Compensation in Coil Intensity Corrected Endorectal MRI

Background: Prostate cancer is one of the most common forms of cancer found in males making early diagnosis important. Magnetic resonance imaging (MRI) has been useful in visualizing and localizing tumor candidates and with the use of endorectal coils (ERC), the signal-to-noise ratio (SNR) can be improved. The coils introduce intensity inhomogeneities and the surface coil intensity correction built into MRI scanners is used to reduce these inhomogeneities. However, the correction typically performed at the MRI scanner level leads to noise amplification and noise level variations. Methods: In this study, we introduce a new Monte Carlo-based noise compensation approach for coil intensity corrected endorectal MRI which allows for effective noise compensation and preservation of details within the prostate. The approach accounts for the ERC SNR profile via a spatially-adaptive noise model for correcting non-stationary noise variations. Such a method is useful particularly for improving the image quality of coil intensity corrected endorectal MRI data performed at the MRI scanner level and when the original raw data is not available. Results: SNR and contrast-to-noise ratio (CNR) analysis in patient experiments demonstrate an average improvement of 11.7 dB and 11.2 dB respectively over uncorrected endorectal MRI, and provides strong performance when compared to existing approaches. Conclusions: A new noise compensation method was developed for the purpose of improving the quality of coil intensity corrected endorectal MRI data performed at the MRI scanner level. We illustrate that promising noise compensation performance can be achieved for the proposed approach, which is particularly important for processing coil intensity corrected endorectal MRI data performed at the MRI scanner level and when the original raw data is not available.Comment: 23 page

Comparison of quality control methods for automated diffusion tensor imaging analysis pipelines

© 2019 Haddad et al. The processing of brain diffusion tensor imaging (DTI) data for large cohort studies requires fully automatic pipelines to perform quality control (QC) and artifact/outlier removal procedures on the raw DTI data prior to calculation of diffusion parameters. In this study, three automatic DTI processing pipelines, each complying with the general ENIGMA framework, were designed by uniquely combining multiple image processing software tools. Different QC procedures based on the RESTORE algorithm, the DTIPrep protocol, and a combination of both methods were compared using simulated ground truth and artifact containing DTI datasets modeling eddy current induced distortions, various levels of motion artifacts, and thermal noise. Variability was also examined in 20 DTI datasets acquired in subjects with vascular cognitive impairment (VCI) from the multi-site Ontario Neurodegenerative Disease Research Initiative (ONDRI). The mean fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were calculated in global brain grey matter (GM) and white matter (WM) regions. For the simulated DTI datasets, the measure used to evaluate the performance of the pipelines was the normalized difference between the mean DTI metrics measured in GM and WM regions and the corresponding ground truth DTI value. The performance of the proposed pipelines was very similar, particularly in FA measurements. However, the pipeline based on the RESTORE algorithm was the most accurate when analyzing the artifact containing DTI datasets. The pipeline that combined the DTIPrep protocol and the RESTORE algorithm produced the lowest standard deviation in FA measurements in normal appearing WM across subjects. We concluded that this pipeline was the most robust and is preferred for automated analysis of multisite brain DTI data

LMMSE Filter Design for MR Image Data

Tato bakalářská práce se zabývá metodikou odstranění šumu v obraze. Zaměřuje se na MRI snímky, na které jsou aplikovány generátory obrazových šumů, a dále se zabývá návrhem LMMSE filtru, který je pak použit na zašuměné obrazy. Byly použity šumy salt and pepper, Gaussův šum a Ricianův šum. Je provedeno objektivní i subjektivní hodnocení provedené filtrace, a to pomocí parametrů SNR, MSE, SSIM, QILV a korelace. Návrh je zpracováván v prostředí Matlabu.This bachelor thesis deals with the method of removing noise in image. It focuses on MRI images where noise generators are applied. The thesis also deals with the LMMSE filter design which is then used for shaded images. Salt and Pepper noise, Gaussian noise and Rican noise are used. An objective and subjective evaluation of the efficiency for each noise type is done by using parameters SNR, MSE, SSIM, QILV and correlation. The design is processed in the Matlab environment.450 - Katedra kybernetiky a biomedicínského inženýrstvívýborn

SPECKLE NOISE REDUCTION USING MULTISCALE LMMSE (MLMMSE)-BASED FILTER

This report presents the project of studying the speckle noise reduction using Multiscale Least Minimum Mean Square Error (MLMMSE) filter. The MLMMSE filter is being compared in terms of feasibility, dependency and stability with the conventional image filter such as LEE 3X3, LEE 5X5, LEE 7X7 and Median filter. The estimation of the MLMMSE filter scheme for the image denoising is being proposed. Together with this project the wavelet selection to determine the best wavelet suit with MLMMSE filter is also being discussed. The principle of the speckle reduction is being used as the MLMMSE filtering are being perform with an undecimated domain wavelet. The image of the adaptive noise will be rescaling from the detail coefficient whereby the amplitude of the image signal will be divided with the variance ratio from the noisy image coefficient to the denoise image. This image is calculated analytically using the properties from the noisy image together with varying the variance and the selected optimal wavelet only. The original image is not resorting in order to obtain the result or to assessing the underlying backscattered signal. Experiment is carried out on normal image being test within two parameter that is Structural Similarity Index (SSIM) and Peak Signal Noise Ratio (PSNR) with varying the variance and the wavelet to identify the most suitable wavelet to run with MLMMSE filter for ultrasound images. The equivalent number of looks (ENL) is analysed in the last part of the experiment to demonstrate visual image quality is achieved for excellency in terms of the dependency of the images itself and also to avoid the typical of impairments of the images which normally created from the critically subsampled in the wavelet-based image denoising

Restoration of DWI Data Using a Rician LMMSE Estimator

This paper introduces and analyzes a linear minimum mean square error (LMMSE) estimator using a Rician noise model and its recursive version (RLMMSE) for the restoration of diffusion weighted images. A method to estimate the noise level based on local estimations of mean or variance is used to automatically parametrize the estimator. The restoration performance is evaluated using quality indexes and compared to alternative estimation schemes. The overall scheme is simple, robust, fast, and improves estimations. Filtering diffusion weighted magnetic resonance imaging (DW-MRI) with the proposed methodology leads to more accurate tensor estimations. Real and synthetic datasets are analyzed

Channel estimation techniques for filter bank multicarrier based transceivers for next generation of wireless networks

A dissertation submitted to Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Master of Science in Engineering (Electrical and Information Engineering), August 2017The fourth generation (4G) of wireless communication system is designed based on the principles of cyclic prefix orthogonal frequency division multiplexing (CP-OFDM) where the cyclic prefix (CP) is used to combat inter-symbol interference (ISI) and inter-carrier interference (ICI) in order to achieve higher data rates in comparison to the previous generations of wireless networks. Various filter bank multicarrier systems have been considered as potential waveforms for the fast emerging next generation (xG) of wireless networks (especially the fifth generation (5G) networks). Some examples of the considered waveforms are orthogonal frequency division multiplexing with offset quadrature amplitude modulation based filter bank, universal filtered multicarrier (UFMC), bi-orthogonal frequency division multiplexing (BFDM) and generalized frequency division multiplexing (GFDM). In perfect reconstruction (PR) or near perfect reconstruction (NPR) filter bank designs, these aforementioned FBMC waveforms adopt the use of well-designed prototype filters (which are used for designing the synthesis and analysis filter banks) so as to either replace or minimize the CP usage of the 4G networks in order to provide higher spectral efficiencies for the overall increment in data rates. The accurate designing of the FIR low-pass prototype filter in NPR filter banks results in minimal signal distortions thus, making the analysis filter bank a time-reversed version of the corresponding synthesis filter bank. However, in non-perfect reconstruction (Non-PR) the analysis filter bank is not directly a time-reversed version of the corresponding synthesis filter bank as the prototype filter impulse response for this system is formulated (in this dissertation) by the introduction of randomly generated errors. Hence, aliasing and amplitude distortions are more prominent for Non-PR. Channel estimation (CE) is used to predict the behaviour of the frequency selective channel and is usually adopted to ensure excellent reconstruction of the transmitted symbols. These techniques can be broadly classified as pilot based, semi-blind and blind channel estimation schemes. In this dissertation, two linear pilot based CE techniques namely the least square (LS) and linear minimum mean square error (LMMSE), and three adaptive channel estimation schemes namely least mean square (LMS), normalized least mean square (NLMS) and recursive least square (RLS) are presented, analyzed and documented. These are implemented while exploiting the near orthogonality properties of offset quadrature amplitude modulation (OQAM) to mitigate the effects of interference for two filter bank waveforms (i.e. OFDM/OQAM and GFDM/OQAM) for the next generation of wireless networks assuming conditions of both NPR and Non-PR in slow and fast frequency selective Rayleigh fading channel. Results obtained from the computer simulations carried out showed that the channel estimation schemes performed better in an NPR filter bank system as compared with Non-PR filter banks. The low performance of Non-PR system is due to the amplitude distortion and aliasing introduced from the random errors generated in the system that is used to design its prototype filters. It can be concluded that RLS, NLMS, LMS, LMMSE and LS channel estimation schemes offered the best normalized mean square error (NMSE) and bit error rate (BER) performances (in decreasing order) for both waveforms assuming both NPR and Non-PR filter banks. Keywords: Channel estimation, Filter bank, OFDM/OQAM, GFDM/OQAM, NPR, Non-PR, 5G, Frequency selective channel.CK201

Imagerie de diffusion en temps-réel (correction du bruit et inférence de la connectivité cérébrale)

La plupart des constructeurs de systèmes d'imagerie par résonance magnétique (IRM) proposent un large choix d'applications de post-traitement sur les données IRM reconstruites a posteriori, mais très peu de ces applications peuvent être exécutées en temps réel pendant l'examen. Mises à part certaines solutions dédiées à l'IRM fonctionnelle permettant des expériences relativement simples ainsi que d'autres solutions pour l'IRM interventionnelle produisant des scans anatomiques pendant un acte de chirurgie, aucun outil n'a été développé pour l'IRM pondérée en diffusion (IRMd). Cependant, comme les examens d'IRMd sont extrêmement sensibles à des perturbations du système hardware ou à des perturbations provoquées par le sujet et qui induisent des données corrompues, il peut être intéressant d'investiguer la possibilité de reconstruire les données d'IRMd directement lors de l'examen. Cette thèse est dédiée à ce projet innovant. La contribution majeure de cette thèse a consisté en des solutions de débruitage des données d'IRMd en temps réel. En effet, le signal pondéré en diffusion peut être corrompu par un niveau élevé de bruit qui n'est plus gaussien, mais ricien ou chi non centré. Après avoir réalisé un état de l'art détaillé de la littérature sur le bruit en IRM, nous avons étendu l'estimateur linéaire qui minimise l'erreur quadratique moyenne (LMMSE) et nous l'avons adapté à notre cadre de temps réel réalisé avec un filtre de Kalman. Nous avons comparé les performances de cette solution à celles d'un filtrage gaussien standard, difficile à implémenter car il nécessite une modification de la chaîne de reconstruction pour y être inséré immédiatement après la démodulation du signal acquis dans l'espace de Fourier. Nous avons aussi développé un filtre de Kalman parallèle qui permet d'appréhender toute distribution de bruit et nous avons montré que ses performances étaient comparables à celles de notre méthode précédente utilisant un filtre de Kalman non parallèle. Enfin, nous avons investigué la faisabilité de réaliser une tractographie en temps-réel pour déterminer la connectivité structurelle en direct, pendant l'examen. Nous espérons que ce panel de développements méthodologiques permettra d'améliorer et d'accélérer le diagnostic en cas d'urgence pour vérifier l'état des faisceaux de fibres de la substance blanche.Most magnetic resonance imaging (MRI) system manufacturers propose a huge set of software applications to post-process the reconstructed MRI data a posteriori, but few of them can run in real-time during the ongoing scan. To our knowledge, apart from solutions dedicated to functional MRI allowing relatively simple experiments or for interventional MRI to perform anatomical scans during surgery, no tool has been developed in the field of diffusion-weighted MRI (dMRI). However, because dMRI scans are extremely sensitive to lots of hardware or subject-based perturbations inducing corrupted data, it can be interesting to investigate the possibility of processing dMRI data directly during the ongoing scan and this thesis is dedicated to this challenging topic. The major contribution of this thesis aimed at providing solutions to denoise dMRI data in real-time. Indeed, the diffusion-weighted signal may be corrupted by a significant level of noise which is not Gaussian anymore, but Rician or noncentral chi. After making a detailed review of the literature, we extended the linear minimum mean square error (LMMSE) estimator and adapted it to our real-time framework with a Kalman filter. We compared its efficiency to the standard Gaussian filtering, difficult to implement, as it requires a modification of the reconstruction pipeline to insert the filter immediately after the demodulation of the acquired signal in the Fourier space. We also developed a parallel Kalman filter to deal with any noise distribution and we showed that its efficiency was quite comparable to the non parallel Kalman filter approach. Last, we addressed the feasibility of performing tractography in real-time in order to infer the structural connectivity online. We hope that this set of methodological developments will help improving and accelerating a diagnosis in case of emergency to check the integrity of white matter fiber bundles.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF