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Temporal slice registration and robust diffusion-tensor reconstruction for improved fetal brain structural connectivity analysis

Bahram Marami, Seyed Sadegh Mohseni Salehi, Onur Afacan, Benoit Scherrer, Caitlin K. Rollins, Edward Yang, Judy A. Estroff, Simon K. Warfield, Ali Gholipour
2017 NeuroImage  
In this paper we introduce a novel robust algorithm to reconstruct in-vivo diffusion-tensor MRI (DTI) of the moving fetal brain and show its effect on structural connectivity analysis.  ...  The results of this study show that slice-level motion correction and robust reconstruction is necessary for reliable in-vivo structural connectivity analysis of the fetal brain.  ...  1 and the CRL spatiotemporal fetal brain MRI atlas 2 developed in the Computational Radiology Laboratory (CRL) at Boston Children's Hospital; and the ANTS software toolkit, N4ITK, and ITKSNAP developed  ... 
doi:10.1016/j.neuroimage.2017.04.033 pmid:28433624 pmcid:PMC5548611 fatcat:cwusoljblvbodfq5unzsbgplzu

A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

Mads Fogtmann, Sharmishtaa Seshamani, Christopher Kroenke, Xi Cheng, Teresa Chapman, Jakob Wilm, Francois Rousseau, Colin Studholme
2014 IEEE Transactions on Medical Imaging  
This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain.  ...  We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment.  ...  The development of comparable diffusion imaging techniques promises to enable similar advances in the study of developing structural connectivity and tissue microstructure in the developing fetal brain  ... 
doi:10.1109/tmi.2013.2284014 pmid:24108711 pmcid:PMC4271809 fatcat:reaqfnwjibgtve2iue3ndxpuxu

Quantifying and modelling tissue maturation in the living human fetal brain

Colin Studholme, François Rousseau
2014 International Journal of Developmental Neuroscience  
The aim of this paper is to provide a review of the current research into MR imaging of the living fetal brain with the aim of motivating improved interfaces between the two fields.  ...  The review begins with a description of faster MRI techniques that are capable of freezing motion of the fetal head during the acquisition of a slice, and how these have been combined with advanced post-processing  ...  is the starting point for many connectivity analysis techniques.  ... 
doi:10.1016/j.ijdevneu.2013.06.006 pmid:23831076 pmcid:PMC4396985 fatcat:jqtub4auzbhy3geviacx4judvm

Dynamic Field Mapping and Motion Correction Using Interleaved Double Spin-Echo Diffusion MRI [chapter]

Jana Hutter, Daan Christiaens, Maria Deprez, Lucilio Cordero-Grande, Paddy Slator, Anthony Price, Mary Rutherford, Joseph V. Hajnal
2017 Lecture Notes in Computer Science  
Diffusion MRI (dMRI) analysis requires the combination of data from many images and this generally requires corrections for image distortion, particularly in regions of varying susceptibility, and for  ...  The method is tested in the challenging environment of fetal dMRI and it is demonstrated using data from 8 pregnant volunteers that combining dynamic distortion correction with slice-by-slice motion correction  ...  connectivity patterns in the brain [6] .  ... 
doi:10.1007/978-3-319-66182-7_60 fatcat:qob7yp32nrawtibxfhiqou7tb4

Mapping Fetal Brain Development In Utero Using Magnetic Resonance Imaging: The Big Bang of Brain Mapping

Colin Studholme
2011 Annual Review of Biomedical Engineering  
dynamically changing fetal brain structure.  ...  For personal use only.  ...  The final reconstruction involves a more complex process that must combine spatially and directionally scattered diffusion measurements made during fetal motion into a single diffusion tensor field on  ... 
doi:10.1146/annurev-bioeng-071910-124654 pmid:21568716 pmcid:PMC3682118 fatcat:bfgd3cj33jfipa67t3ssm3x4ry

In utero diffusion tensor imaging of the fetal brain: A reproducibility study

András Jakab, Ruth Tuura, Christian Kellenberger, Ianina Scheer
2017 NeuroImage: Clinical  
To achieve robust results for the quantitative analysis of diffusivity and anisotropy values, fetal-specific image processing is recommended and repeated DTI is needed to ensure the detectability of fiber  ...  Our purpose was to evaluate the within-subject reproducibility of in utero diffusion tensor imaging (DTI) metrics and the visibility of major white matter structures.  ...  Future directions of fetal imaging research should emphasize the more robust reconstruction of the diffusion tensor based on repeated data and higher angular resolution acquisition schemes.  ... 
doi:10.1016/j.nicl.2017.06.013 pmid:28652972 pmcid:PMC5477067 fatcat:4rabfgpelva65k4awyuqqmrbza

In Utero Diffusion Tensor Imaging Of The Fetal Brain: A Reproducibility Study [article]

Andras Jakab, Ruth Tuura, Christian Kellenberger, Ianina Scheer
2017 bioRxiv   pre-print
To achieve robust results for the quantitative analysis of diffusivity and anisotropy values, fetal-specific image processing is recommended and repeated DTI is needed to ensure the detectability of fiber  ...  Our purpose was to evaluate the within-subject reproducibility of in utero diffusion tensor imaging (DTI) metrics and the visibility of major white matter structures.  ...  Future directions of fetal imaging research should emphasize the more robust reconstruction of the diffusion tensor based on repeated data and higher angular resolution acquisition schemes.  ... 
doi:10.1101/132704 fatcat:lrut4rqtnzgy7dqoqccoeztnxy

A Tetrahedron-Based Heat Flux Signature for Cortical Thickness Morphometry Analysis [chapter]

Yonghui Fan, Gang Wang, Natasha Lepore, Yalin Wang
2018 Lecture Notes in Computer Science  
Perfusion and Fetal Blood Oxygen Saturation in Normal Pregnancy and Placental Insufficiency 330 Stochastic Deep Compressive Sensing for the Reconstruction of Diffusion Tensor Cardiac MRI 333 Local and  ...  Normalisation 559 Exploring Fiber Skeletons via Joint Representation of Functional Networks and Structural Connectivity 560 Ultra-fast T2-weighted MR Reconstruction using Complementary T1-weighted Information  ... 
doi:10.1007/978-3-030-00931-1_48 pmid:30338317 pmcid:PMC6191198 fatcat:dqhvpm5xzrdqhglrfftig3qejq

Front Matter: Volume 12032

Ivana Išgum, Olivier Colliot
2022 Medical Imaging 2022: Image Processing  
Utilization of CIDs allows articles to be fully citable as soon as they are published online, and connects the same identifier to all online and print versions of the publication.  ...  using a Base 36 numbering system employing both numerals and letters.  ...  for thermal damage model analysis and optimization in brain laser interstitial thermal therapy [12032-133] 12032 3T Substantia nigra analysis by tensor decomposition of T2-weighted images for Parkinson's  ... 
doi:10.1117/12.2638192 fatcat:ikfgnjefaba2tpiamxoftyi6sa

Front Matter: Volume 9784

2016 Medical Imaging 2016: Image Processing  
Rb-82 PET/CTs [9784-4] 9784 06 Combining the boundary shift integral and tensor-based morphometry for brain atrophy estimation [9784-5] SESSION 2 KEYNOTE AND DIFFUSION MRI 9784 07 Image-processing pipelines  ...  ] 9784 0S Robust group-wise rigid registration of point sets using t-mixture model [9784-27] 9784 0T Multi-region statistical shape model for cochlear implantation [9784-28] iv Proc. of SPIE Vol. 9784  ...  using a probabilistic mixture model [9784-117] POSTER SESSION: DIFFUSION/FUNCTIONAL MRI AND BRAIN CONNECTIVITY 9784 3C Rotationally invariant clustering of diffusion MRI data using spherical harmonics  ... 
doi:10.1117/12.2240619 fatcat:kot6cogf4rf6dcjhkzdrr5gahi

Scattered slice SHARD reconstruction for motion correction in multi-shell diffusion MRI [article]

Daan Christiaens, Lucilio Cordero-Grande, Maximilian Pietsch, Jana Hutter, Anthony N. Price, Emer J. Hughes, Katy Vecchiato, Maria Deprez, A. David Edwards, Joseph V. Hajnal, J-Donald Tournier
2020 arXiv   pre-print
Diffusion MRI offers a unique probe into neural microstructure and connectivity in the developing brain.  ...  However, analysis of neonatal brain imaging data is complicated by inevitable subject motion, leading to a series of scattered slices that need to be aligned within and across diffusion-weighted contrasts  ...  As such, the reconstructed output data can be passed on to subsequent processing pipelines for subject-level and group-level analysis of tissue miscrostructure and connectivity in the developing brain  ... 
arXiv:1905.02996v2 fatcat:xtxreyf7gbaarodlfvv5peehuq

Slice-level diffusion encoding for motion and distortion correction

Jana Hutter, Daan J Christiaens, Torben Schneider, Lucilio Cordero-Grande, Paddy J Slator, Maria Deprez, Anthony N Price, J-Donald Tournier, Mary Rutherford, Joseph V Hajnal
2018 Medical Image Analysis  
By enabling free choice of the diffusion encoding on the slice level, a higher temporal sampling of slices with low b-value can be achieved.  ...  Advances in microstructural modelling are leading to growing requirements on diffusion MRI acquisitions, namely sensitivity to smaller structures and better resolution of the geometric orientations.  ...  His research interests include image processing, quantitative analysis, and microstructural modelling in neonatal and fetal diffusion MRI.  ... 
doi:10.1016/j.media.2018.06.008 pmid:29966941 pmcid:PMC6191883 fatcat:mfxhzz5utjdyzfvzb7zicsswtu

White matter maturation of normal human fetal brain. An in vivo diffusion tensor tractography study

Emilie Zanin, Jean-Philippe Ranjeva, Sylviane Confort-Gouny, Maxime Guye, Daniele Denis, Patrick J. Cozzone, Nadine Girard
2011 Brain and Behavior  
diffusion tensor imaging (DTI) tractography.  ...  for each WM bundle type.  ...  for analysis.  ... 
doi:10.1002/brb3.17 pmid:22399089 pmcid:PMC3236541 fatcat:f5ezu7vlqbalpnfuxakwf6riha

MR imaging methods for assessing fetal brain development

Mary Rutherford, Shuzhou Jiang, Joanna Allsop, Lucinda Perkins, Latha Srinivasan, Tayyib Hayat, Sailesh Kumar, Jo Hajnal
2008 Developmental Neurobiology  
Fetal magnetic resonance imaging provides an ideal tool for investigating growth and development of the brain in vivo.  ...  Current imaging methods have been hampered by fetal motion but recent advances in image acquisition can produce high signal to noise, high resolution 3-dimensional datasets suitable for objective quantification  ...  We would like to thank the Medical Research Council, The Health Foundation, Philips Medical Systems, Action for Medical Research and The European Leucodystrophy Association for their support.  ... 
doi:10.1002/dneu.20614 pmid:18383541 fatcat:6eenfhspt5flnesko7ypuh2ywi

Multi‐modal functional MRI to explore placental function over gestation

Jana Hutter, Paddy J. Slator, Laurence Jackson, Ana Dos Santos Gomes, Alison Ho, Lisa Story, Jonathan O'Muircheartaigh, Rui P. A. G. Teixeira, Lucy C. Chappell, Daniel C. Alexander, Mary A. Rutherford, Joseph V. Hajnal
2018 Magnetic Resonance in Medicine  
To investigate, visualize and quantify the physiology of the human placenta in several dimensions - functional, temporal over gestation, and spatial over the whole organ.  ...  ACKNOWLEDGMENTS The authors thank all mothers for taking part and acknowledge the help of all involved midwives, obstetricians and administrators.  ...  Translations between subsequent echos were reported as minimal for fetal brain MEGE 38 and are even smaller for the placenta, which does not experience autonomous movement but mostly slow respiratory  ... 
doi:10.1002/mrm.27447 pmid:30242899 pmcid:PMC6585747 fatcat:r77fgrj7pnbb5dy32b4xrjzayy
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