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Gibbs ringing in diffusion MRI

Jelle Veraart, Els Fieremans, Ileana O. Jelescu, Florian Knoll, Dmitry S. Novikov
2015 Magnetic Resonance in Medicine  
Purpose-To study and reduce the effect of Gibbs ringing artifact on computed diffusion parameters.  ...  full suppression of Gibbs ringing, and the absence of staircasing artifacts typical for total variation methods.  ...  Indeed, Gibbs ringing is an artifactual feature of the signal that will corrupt all metrics derived from it.  ... 
doi:10.1002/mrm.25866 pmid:26257388 pmcid:PMC4915073 fatcat:kawdlja7tjd35hci3sw5t6rjey

Training a Neural Network for Gibbs and Noise Removal in Diffusion MRI [article]

Matthew J. Muckley, Benjamin Ades-Aron, Antonios Papaioannou, Gregory Lemberskiy, Eddy Solomon, Yvonne W. Lui, Daniel K. Sodickson, Els Fieremans, Dmitry S. Novikov, Florian Knoll
2019 arXiv   pre-print
The CNN for complex images was also able to reduce artifacts in partial Fourier acquisitions. The proposed CNNs extend the ability of artifact correction in diffusion MRI.  ...  Both models were based on the same encoder-decoder structure and were trained by simulating MRI acquisitions on synthetic non-MRI images.  ...  Diffusion MRI is an intriguing test application for Gibbs and noise removal models. Both effects can have drastic effects on diffusion parameter maps.  ... 
arXiv:1905.04176v2 fatcat:ebtwn7mfm5asbasdxrcjkxxlji

Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline

Benjamin Ades-Aron, Jelle Veraart, Peter Kochunov, Stephen McGuire, Paul Sherman, Elias Kellner, Dmitry S. Novikov, Els Fieremans
2018 NeuroImage  
Following this processing pipeline, iterative parameter estimation techniques were used to derive diffusion parameters of interest based on the diffusion tensor and kurtosis tensor.  ...  variability including: thermal noise, Gibbs ringing artifacts, Rician bias, EPI and eddy current induced spatial distortions, and motion-related artifacts.  ...  ACKNOWLEGEMENTS The authors would like to thank Dr. Jesper Andersson and Dr. Steve Smith for their helpful discussion and correspondence during the production of thus work.  ... 
doi:10.1016/j.neuroimage.2018.07.066 pmid:30077743 pmcid:PMC6371781 fatcat:yjzozy6qrzfmleg2tqxoyx6tmy

Evaluating corrections for Eddy-currents and other EPI distortions in diffusion MRI: methodology and a dataset for benchmarking

M. Okan Irfanoglu, Joelle Sarlls, Amritha Nayak, Carlo Pierpaoli
2018 Magnetic Resonance in Medicine  
To propose a methodology for assessment of algorithms that correct distortions due to motion, eddy-currents, and echo planar imaging in diffusion weighted images (DWIs).  ...  The third confound indirectly affected by phaseencoding are the Gibbs ringing artifacts.  ...  Therefore, one needs to rely on the DWI data itself to derive measures of correction quality.  ... 
doi:10.1002/mrm.27577 pmid:30394561 pmcid:PMC6518940 fatcat:b2wqch554ja3pnclqjt2jowfre

Apparent Diffusion Coefficient Assessment of Brain Development in Normal Fetuses and Ventriculomegaly

Maria Giovanna Di Trani, Lucia Manganaro, Amanda Antonelli, Michele Guerreri, Riccardo De Feo, Carlo Catalano, Silvia Capuani
2019 Frontiers in Physics  
All images were corrected for noise, Gibbs-ringing, and motion artifacts. The signal-to-noise ratio (SNR) was calculated and the ADC was measured with a linear least-squared algorithm.  ...  Diffusion neuro-MRI has benefited significantly from sophisticated pre-processing procedures aimed at improving image quality and diagnostic.  ...  Our ADC values were in good accordance with the measurements derived from the contribution of solely diffusion in the IVIM study [21] , suggesting that our acquisition strategy effectively minimized perfusion  ... 
doi:10.3389/fphy.2019.00160 fatcat:grnoujckkzc4jlpjq6xdxw2m4i

Q-space truncation and sampling in diffusion spectrum imaging

Qiyuan Tian, Ariel Rokem, Rebecca D. Folkerth, Aapo Nummenmaa, Qiuyun Fan, Brian L. Edlow, Jennifer A. McNab
2016 Magnetic Resonance in Medicine  
To minimize the effects of Gibbs ringing, ODFs should be reconstructed from unfiltered q-space data with the integration length over the PDF constrained to around the MDD. Magn Reson Med 000:000-000,  ...  Results: Both ex vivo and in vivo data showed Gibbs ringing in PDFs, which becomes the main source of artifact in the subsequently reconstructed ODFs.  ...  Larry Wald, Boris Keil, and Thomas Witzel for their advice and assistance with the experimental setup. We thank Drs.  ... 
doi:10.1002/mrm.26071 pmid:26762670 pmcid:PMC4942411 fatcat:2nionok77vbotj4xjjxehq6mhi

Measuring non-parametric distributions of intravoxel mean diffusivities using a clinical MRI scanner

Alexandru V. Avram, Joelle E. Sarlls, Peter J. Basser
2019 NeuroImage  
We analyze the measured IDE signal decays using a regularized inverse laplace transform (ILT) to derive a probability distribution of mean diffusivities of tissue water in each voxel.  ...  Based on numerical simulations we assess the sensitivity and accuracy of our ILT analysis and optimize an experimental protocol for use with clinical MRI scanners.  ...  of Child Health and Human Development (NICHD) within the National Institutes of Health (NIH).  ... 
doi:10.1016/j.neuroimage.2018.10.030 pmid:30326294 pmcid:PMC6289178 fatcat:ouzwnzvgunhutp5pfazasykgtu

Fiberfox: An Extensible System for Generating Realistic White Matter Software Phantoms [chapter]

Peter F. Neher, Frederik B. Laun, Bram Stieltjes, Klaus H. Maier-Hein
2013 Mathematics and Visualization  
To demonstrate the relevance of Fiberfox for current research questions, we reveal the adverse effects of anisotropic voxels on the outcome of 11 different fiber tractography algorithms.  ...  Gibbs ringing, N=2 ghosting and susceptibility distortions.  ...  The k-space signal can thus be calculated by O S.k/ D Z .r/e i.krC .t TE;r// dr Fig. 1 1 Artifacts included in Fiberfox: Illustration of Rician noise (a), blurring (b) and Gibbs ringing (c) artifacts  ... 
doi:10.1007/978-3-319-02475-2_10 fatcat:nks42xhm3ram7i7qs3yifqqcj4

D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data

Daniele Perrone, Ben Jeurissen, Jan Aelterman, Timo Roine, Jan Sijbers, Aleksandra Pizurica, Alexander Leemans, Wilfried Philips, Christophe Lenglet
2016 PLoS ONE  
In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail.  ...  Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues.  ...  that support the NIH Blueprint for Neuroscience Research; and by the McDonnell Center for Systems Neuroscience at Washington University for providing part of the data.  ... 
doi:10.1371/journal.pone.0149778 pmid:26930054 pmcid:PMC4773122 fatcat:5o5k6goiqbg5nfvlrmkav7qsf4

DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) method for correcting echo planar imaging distortions

M. Okan Irfanoglu, Pooja Modi, Amritha Nayak, Elizabeth B. Hutchinson, Joelle Sarlls, Carlo Pierpaoli
2015 NeuroImage  
Imposing the theoretical "blip-up blipdown distortion symmetry" may not be appropriate in the presence of common clinical scanning artifacts such as motion, ghosting, Gibbs ringing, vibrations, and low  ...  DR-BUDDI can incorporate information from an undistorted structural MRI and also use diffusion-weighted images (DWI) to guide the registration, improving the quality of the registration in the presence  ...  To assess the effects of Gibbs ringing artifacts on DR-BUDDI correction, a data set from Test Set 3 with particularly evident signal pile-ups was selected.  ... 
doi:10.1016/j.neuroimage.2014.11.042 pmid:25433212 pmcid:PMC4286283 fatcat:stvoupvypjaklfubhpqd4mdwja

MK-curve - Characterizing the relation between mean kurtosis and alterations in the diffusion MRI signal

Fan Zhang, Lipeng Ning, Lauren J. O'Donnell, Ofer Pasternak
2019 NeuroImage  
While DKI measures are sensitive to tissue alterations, they are also affected by signal alterations caused by imaging artifacts such as noise, motion and Gibbs ringing.  ...  Diffusion kurtosis imaging (DKI) is a diffusion MRI (dMRI) technique to quantify brain microstructural properties.  ...  ACKNOWLEDGMENT: The authors would like to thank the NYU Diffusion MRI group (WLLS DKI model fit, constrained fit and MPPCA), Dr.  ... 
doi:10.1016/j.neuroimage.2019.04.015 pmid:30978492 pmcid:PMC6592693 fatcat:udqkm5fnpjhpjjuuiouswtnepa

Miniature pig magnetic resonance spectroscopy model of normal adolescent brain development

Meghann C. Ryan, Peter Kochunov, Paul M. Sherman, Laura M. Rowland, S. Andrea Wijtenburg, Ashley Acheson, L. Elliot Hong, John Sladky, Stephen McGuire
2018 Journal of Neuroscience Methods  
changes in metabolites to WM integrity measurements derived from diffusion weighted imaging (DWI) [38, 39] .  ...  We analyzed longitudinal changes in adolescent pigs using proton magnetic resonance spectroscopy ( 1 H-MRS) and examined the relationship with white matter (WM) integrity derived from diffusion weighted  ...  Acknowledgments The authors wish to thank Ms. Elaine  ... 
doi:10.1016/j.jneumeth.2018.08.008 pmid:30099002 pmcid:PMC6211793 fatcat:23khsczrvbbbfemyzbkudqxidy

Early childhood bilingualism: effects on brain structure and function

Sezgi Goksan, Froso Argyri, Jonathan D. Clayden, Frederique Liegeois, Li Wei
2020 F1000Research  
We will compare connectivity measures and attention skills between monolinguals and bilinguals to examine the effects of bilingual exposure.  ...  We will collect structural and functional MRI, and quantitative measures of EC and language skills from two groups of English-Greek bilingual children - 20 simultaneous bilinguals (exposure to both languages  ...  We also thank Professor Chris Clark for providing integral support and access to the MRI scanner.  ... 
doi:10.12688/f1000research.23216.2 fatcat:wc6ucsmn2zfxlgni5vyjxepqua

Denoising of diffusion MRI using random matrix theory

Jelle Veraart, Dmitry S. Novikov, Daan Christiaens, Benjamin Ades-aron, Jan Sijbers, Els Fieremans
2016 NeuroImage  
By exploiting the intrinsic redundancy in diffusion MRI using universal properties of the eigenspectrum of random covariance matrices, we remove noise-only principal components, thereby enabling signal-to-noise  ...  By studying statistics of residuals, we demonstrate that the technique suppresses local signal fluctuations that solely originate from thermal noise rather than from other sources such as anatomical detail  ...  Figure 10 . 10 Effect of denoising on the variability in the estimated MD [μm 2 /ms] and FA as function of the denoising method and the number of measurements Author manuscript; available in PMC 2017 November  ... 
doi:10.1016/j.neuroimage.2016.08.016 pmid:27523449 pmcid:PMC5159209 fatcat:md73iuthojaqjaflhmv2mqmeii

Transient Anomalous Diffusion MRI in Excised Mouse Spinal Cord: Comparison Among Different Diffusion Metrics and Validation With Histology

Alessandra Caporale, Giovanni Battista Bonomo, Giulio Tani Raffaelli, Ada Maria Tata, Bice Avallone, Felix Werner Wehrli, Silvia Capuani
2022 Frontiers in Neuroscience  
The normal diffusion of bulk water in tissues is not able to detect the specific features of a complex system, providing nonlocal, diffusion measurement averaged on a 10-20 μm length scale.  ...  Axon diameter (AxDiam), the standard deviation of diameters (SDax.diam), axonal density (AxDens) and effective local density (ELD) were extracted from optical images in several WM tracts.  ...  All authors contributed to the article and approved the submitted version.  ... 
doi:10.3389/fnins.2021.797642 pmid:35242002 pmcid:PMC8885723 fatcat:rpdgfauc4jdirfslnam2jlfkmi
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