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Learning a Reliable Estimate of the Number of Fiber Directions in Diffusion MRI [chapter]

Thomas Schultz
2012 Lecture Notes in Computer Science  
Having to determine an adequate number of fiber directions is a fundamental limitation of multi-compartment models in diffusion MRI.  ...  The method is shown to result in plausible and reproducible decisions on three repeated scans of the same subject.  ...  Introduction Multi-compartment models are a traditional way of estimating more than a single fiber orientation in diffusion MRI [1, 2] .  ... 
doi:10.1007/978-3-642-33454-2_61 fatcat:jho7dxi5yzdgjjcirzf53mfq4e

Design and Validation of Diffusion MRI Models of White Matter

Ileana O. Jelescu, Matthew D. Budde
2017 Frontiers in Physics  
Frontiers in Physics | www.frontiersin.org  ...  AUTHOR CONTRIBUTIONS All authors listed have made a substantial, direct, and intellectual contribution to the work, and approved it for publication.  ...  In practice, DIAMOND uses an iterative approach in defining the number of compartments in each voxel.  ... 
doi:10.3389/fphy.2017.00061 pmid:29755979 pmcid:PMC5947881 fatcat:ai6ejv6rzfe55i4tl64l5dihem

Identification of Gadolinium Contrast Enhanced Regions in MS Lesions Using Brain Tissue Microstructure Information Obtained from Diffusion and T2 Relaxometry MRI [chapter]

Sudhanya Chatterjee, Olivier Commowick, Onur Afacan, Simon K. Warfield, Christian Barillot
2018 Lecture Notes in Computer Science  
However in non-contrast enhanced structural magnetic resonance imaging (MRI) the regions of the lesion undergoing active BBB breakdown cannot be distinguished from the other parts of the lesion.  ...  We thus propose a framework to predict enhancing regions in MS lesions using tissue microstructure information derived from T2 relaxometry and diffusion MRI (dMRI) multicompartment models.  ...  Simultaneous estimation of the weights and parameters of the distributions of such multi-compartment models is nontrivial and not reliable in terms of robustness and accuracy [13] .  ... 
doi:10.1007/978-3-030-00931-1_8 fatcat:nigjjqxwn5hzffr4twzwqcg2fa

The Diffusion-Simulated Connectivity (DiSCo) Dataset

Jonathan Rafael-Patino, Gabriel Girard, Raphaël Truffet, Marco Pizzolato, Emmanuel Caruyer, Jean-Philippe Thiran
2021 Data in Brief  
The methodological development in the mapping of the brain structural connectome from diffusion-weighted magnetic resonance imaging (DW-MRI) has raised many hopes in the neuroscientific community.  ...  The simulated images capture the microscopic properties of the tissue (e.g. fibre diameter, water diffusing within and around fibres, free water compartment), while also having desirable macroscopic properties  ...  This project has received funding from the Swiss National Science Foundation under grant number 205320_175974 and Spark grant number 190297 .  ... 
doi:10.1016/j.dib.2021.107429 pmid:34632021 pmcid:PMC8487002 fatcat:xd6duyomsvfzzkeobljjjb4qp4

A model describing diffusion in prostate cancer

Nima Gilani, Paul Malcolm, Glyn Johnson
2016 Magnetic Resonance in Medicine  
The model satisfactorily explains the variability of ADC estimates found in the literature.  ...  Here prostate diffusion is analyzed in terms of a model that takes explicit account of tissue compartmentalization, exchange effects and the non-Gaussian behaviour of tissue diffusion.  ...  However, to date the heterogeneity of prostate tissue has not generally been taken into account and MRI parameter estimates represent a weighted average of the contributions of the different compartments  ... 
doi:10.1002/mrm.26340 pmid:27439379 fatcat:tgxv6vpluranxoqsfxrz4uyejq

Optimal Model Mapping for Intravoxel Incoherent Motion MRI

Yen-Peng Liao, Shin-ichi Urayama, Tadashi Isa, Hidenao Fukuyama
2021 Frontiers in Human Neuroscience  
This study proposed an optimal model mapping method to improve the reliability of the perfusion parameter estimation in the IVIM study.  ...  The quality of the diffusion analysis can influence the reliability of the perfusion analysis.  ...  Matsuhashi for their comments that greatly improved the manuscript. We also thank the University of Minnesota Center for Magnetic Resonance Research for sharing their Multiband DWI sequence.  ... 
doi:10.3389/fnhum.2021.617152 pmid:33692677 pmcid:PMC7937866 fatcat:u2jc3rasrvh3honqqq5ldapeji

Separating blood and water: Perfusion and free water elimination from diffusion MRI in the human brain

Anna S. Rydhög, Filip Szczepankiewicz, Ronnie Wirestam, André Ahlgren, Carl-Fredrik Westin, Linda Knutsson, Ofer Pasternak
2017 NeuroImage  
The influence of the vascular compartment on the estimation of the free water fraction and other diffusivities was investigated by simulating perfusion in diffusion MRI data.  ...  Free water estimates from diffusion MRI are assumed to account for freely diffusing water molecules in the extracellular space, but may be biased by other pools of molecules in rapid random motion, such  ...  The number of directions per shell was chosen since six directions (in addition to a baseline) is the minimal angular resolution required to estimate a diffusion tensor.  ... 
doi:10.1016/j.neuroimage.2017.04.023 pmid:28412443 pmcid:PMC5548601 fatcat:vnvpw4uaebbvhnmu2s3ugiprou

Isotropic non-white matter partial volume effects in constrained spherical deconvolution

Timo Roine, Ben Jeurissen, Daniele Perrone, Jan Aelterman, Alexander Leemans, Wilfried Philips, Jan Sijbers
2014 Frontiers in Neuroinformatics  
Diffusion-weighted (DW) magnetic resonance imaging (MRI) is a non-invasive imaging method, which can be used to investigate neural tracts in the white matter (WM) of the brain.  ...  In addition, a low diffusion weighting or SNR increases the effects. The non-WM PVEs may cause problems in connectomics, where reliable fiber tracking at the WM-GM interface is especially important.  ...  ACKNOWLEDGMENTS This work was supported by the Fund for Scientific Research-Flanders (FWO), and by the Interuniversity Attraction Poles Program (P7/11) initiated by the Belgian Science Policy Office.  ... 
doi:10.3389/fninf.2014.00028 pmid:24734018 pmcid:PMC3975100 fatcat:nuebjjw45jarhns7ztxoqxqury

Image Downsampling Expedited Adaptive Least-squares (IDEAL) fitting improves intravoxel incoherent motion (IVIM) analysis in the human kidney [article]

Julia Stabinska, Helge Jorn Zollner, Thomas Andreas Thiel, Hans-Jorg Wittsack, Alexandra Ljimani
2022 bioRxiv   pre-print
Purpose: To improve the reliability of intravoxel incoherent motion model (IVIM) parameter estimation for the diffusion-weighted imaging in the kidney using a novel Image Downsampling Expedited Adaptive  ...  Thus, the IDEAL approach has the potential to improve the reliability of renal DW-MRI analysis for clinical applications.  ...  Acknowledgement The study was supported by a grant from the German Research Foundation (DFG)(Project number: 408765040).  ... 
doi:10.1101/2022.06.09.495469 fatcat:45plzroagfcizm2n7eivz5xi4q

Comprehensive Maximum Likelihood Estimation of Diffusion Compartment Models Towards Reliable Mapping of Brain Microstructure [chapter]

Aymeric Stamm, Olivier Commowick, Simon K. Warfield, S. Vantini
2016 Lecture Notes in Computer Science  
Diffusion MRI is a key in-vivo non invasive imaging capability that can probe the microstructure of the brain.  ...  Diffusion Compartment (DC) models divide the voxel into smaller compartments in which diffusion is homogeneous.  ...  In addition, notwithstanding S 0 and τ 2 are not diffusion parameters, their accurate knowledge is critical for a reliable estimation of the diffusion parameters.  ... 
doi:10.1007/978-3-319-46726-9_72 fatcat:d6p2acyihfc4djvxwkjx632qm4

Test-retest reliability and long-term stability of 3-tissue constrained spherical deconvolution methods for analyzing diffusion MRI data [article]

Benjamin T Newman, Thijs Dhollander, Kristen A Reynier, Matthew B Panzer, Thomas Jason Druzgal
2019 bioRxiv   pre-print
Methods: This study examined estimates of whole brain microstructure for the three tissue compartments, in three separate test-retest cohorts.  ...  Conclusion: The 3-tissue CSD techniques provide reliable and stable estimates of tissue microstructure composition, up to 3 months longitudinally in a control population.  ...  Acknowledgements NITRC, NITRC-IR, and NITRC-CE have been funded in whole or in part with Federal funds from the Department of Health and Human Services, National Institute of Biomedical Imaging and Bioengineering  ... 
doi:10.1101/764506 fatcat:tun2pwzjivbvtafgvrd2bghvum

Multi-Diffusion-Tensor Fitting via Spherical Deconvolution: A Unifying Framework [chapter]

Thomas Schultz, Carl-Fredrik Westin, Gordon Kindlmann
2010 Lecture Notes in Computer Science  
In analyzing diffusion magnetic resonance imaging, multitensor models address the limitations of the single diffusion tensor in situations of partial voluming and fiber crossings.  ...  Our work demonstrates the benefits of unifying previously divergent lines of work in diffusion image analysis.  ...  The authors would like to thank Alfred Anwander (MPI CBS, Leipzig, Germany) for providing data used in this work.  ... 
doi:10.1007/978-3-642-15705-9_82 fatcat:wqumevnsvfge7fdbgc7pp53im4

The sensitivity of diffusion MRI to microstructural properties and experimental factors

Maryam Afzali, Tomasz Pieciak, Sharlene Newman, Eleftherios Garifallidis, Evren Özarslan, Hu Cheng, Derek K Jones
2020 Journal of Neuroscience Methods  
The sensitivity of the diffusion MRI signal to the microstructural components and the effects of curvedness of axonal trajectories on the diffusion signal are reviewed.  ...  In this paper, we first give an introduction to diffusion MRI and different encoding schemes. Then, signal representation-based methods and multi-compartment models are briefly explained.  ...  Acknowledgements The data used for  ... 
doi:10.1016/j.jneumeth.2020.108951 pmid:33017644 pmcid:PMC7762827 fatcat:oi3x6utivvh6pbqalmbg3zr5tm

Axon Diameter Index Estimation Independent of Fiber Orientation Distribution Using High-Gradient Diffusion MRI

Qiuyun Fan, Aapo Nummenmaa, Thomas Witzel, Ned Ohringer, Qiyuan Tian, Kawin Setsompop, Eric C. Klawiter, Bruce R. Rosen, Lawrence L. Wald, Susie Y. Huang
2020 NeuroImage  
Axon diameter mapping using high-gradient diffusion MRI has generated great interest as a noninvasive tool for studying trends in axonal size in the human brain.  ...  This approach is shown to significantly benefit from the use of real-valued diffusion data with Gaussian noise, which reduces the systematic bias in the estimated parameters resulting from the elevation  ...  We also thank the reviewers of the manuscript for their valuable suggestions and explanations, which have served to improve the overall presentation and content of this manuscript.  ... 
doi:10.1016/j.neuroimage.2020.117197 pmid:32745680 pmcid:PMC7736138 fatcat:6jogyna34zf55dghjvyhd6hy4y

Application of stereological estimates in patients with severe head injuries using CT and MR scanning images

N Eriksen, E Rostrup, K Andersen, M J Lauritzen, M Fabricius, V A Larsen, J P Dreier, A J Strong, J A Hartings, B Pakkenberg
2010 British Journal of Radiology  
The reliability of the estimates was tested by obtaining repeated intra-and interobserver estimates of selected subdivisions of the brain in patients with acute head injury, as well as in an MR phantom  ...  The estimates of different subdivisions showed a coefficient of variation (CV) below 12% in the patients and below 7% for phantom estimation.  ...  This could be caused by differences in the definitions of the various compartments in histology/ MRI or by the small number of cases in this study.  ... 
doi:10.1259/bjr/18575224 pmid:19690078 pmcid:PMC3473455 fatcat:5qfn7pzk4ncrrif43wxjtv3zra
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