Multi-contrast human neonatal brain atlas: application to normal neonate development analysis.

doi:10.1016/J.NEUROIMAGE.2011.01.051

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Multi-contrast human neonatal brain atlas: application to normal neonate development analysis.

Journal Article•DOI•

Multi-contrast human neonatal brain atlas: application to normal neonate development analysis.

Kenichi Oishi¹, Susumu Mori², Susumu Mori¹, Pamela Donohue¹, Thomas Ernst³, Lynn Anderson³, Steven Buchthal³, Andreia V. Faria¹, Hangyi Jiang¹, Hangyi Jiang², Xin Li¹, Michael I. Miller¹, Peter C.M. van Zijl¹, Peter C.M. van Zijl², Linda Chang³ - Show less +11 more•Institutions (3)

Johns Hopkins University School of Medicine¹, Kennedy Krieger Institute², University of Hawaii at Manoa³

01 May 2011-NeuroImage (Neuroimage)-Vol. 56, Iss: 1, pp 8-20

TL;DR: The development of neonatal brain atlases with detailed anatomic information derived from DTI and co-registered anatomical MRI and a diffeomorphic transformation is reported, which was able to normalize Neonatal brain images to the atlas space and three-dimensionally parcellate images into 122 regions.

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About: This article is published in NeuroImage.The article was published on 2011-05-01 and is currently open access. It has received 287 citations till now. The article focuses on the topics: Diffusion MRI.

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Journal Article•DOI•

Co-Planar Stereotaxic Atlas of the Human Brain—3-Dimensional Proportional System: An Approach to Cerebral Imaging, J. Talairach, P. Tournoux. Georg Thieme Verlag, New York (1988), 122 pp., 130 figs. DM 268

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M.J. Torrens

01 Mar 1990-Clinical Radiology

9,362 citations

Journal Article•DOI•

The early development of brain white matter: A review of imaging studies in fetuses, newborns and infants

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Jessica Dubois¹, Ghislaine Dehaene-Lambertz¹, Sofya Kulikova², Cyril Poupon, Petra Susan Hüppi³, Lucie Hertz-Pannier², Lucie Hertz-Pannier¹ - Show less +3 more•Institutions (3)

French Institute of Health and Medical Research¹, Paris Descartes University², Harvard University³

12 Sep 2014-Neuroscience

TL;DR: Current knowledge from post-mortem descriptions and in vivo MRI studies is summed up, focusing on T1- and T2-weighted imaging, diffusion tensor imaging, and quantitative mapping of T1/T2 relaxation times, myelin water fraction and magnetization transfer ratio.

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604 citations

Cites background from "Multi-contrast human neonatal brain..."

...The interest of DTI studies rests in the quantification of differences across WM bundles, detailing a progression of maturation from a central-to-peripheral and a posterior-to-anterior direction (Oishi et al., 2011)....
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Journal Article•DOI•

The Neonatal Connectome During Preterm Brain Development

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Martijn P. van den Heuvel¹, Karina J. Kersbergen¹, Marcel A. de Reus¹, Kristin Keunen¹, René S. Kahn¹, Floris Groenendaal¹, Linda S. de Vries¹, Manon J.N.L. Benders¹ - Show less +4 more•Institutions (1)

Utrecht University¹

01 Sep 2015-Cerebral Cortex

TL;DR: It is concluded that hallmark organizational structures of the human connectome are present before term birth and subject to early development.

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Abstract: The human connectome is the result of an elaborate developmental trajectory. Acquiring diffusion-weighted imaging and resting-state fMRI, we studied connectome formation during the preterm phase of macroscopic connectome genesis. In total, 27 neonates were scanned at week 30 and/or week 40 gestational age (GA). Examining the architecture of the neonatal anatomical brain network revealed a clear presence of a small-world modular organization before term birth. Analysis of neonatal functional connectivity (FC) showed the early formation of resting-state networks, suggesting that functional networks are present in the preterm brain, albeit being in an immature state. Moreover, structural and FC patterns of the neonatal brain network showed strong overlap with connectome architecture of the adult brain (85 and 81%, respectively). Analysis of brain development between week 30 and week 40 GA revealed clear developmental effects in neonatal connectome architecture, including a significant increase in white matter microstructure (P < 0.01), small-world topology (P < 0.01) and interhemispheric FC (P < 0.01). Computational analysis further showed that developmental changes involved an increase in integration capacity of the connectivity network as a whole. Taken together, we conclude that hallmark organizational structures of the human connectome are present before term birth and subject to early development.

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314 citations

Cites background or methods from "Multi-contrast human neonatal brain..."

...A detailed description of this neonatal template, including information and illustrations on the 56 regions and an open access copy of the template, is presented in the paper of Oishi et al. (2011)....
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...For comparison to the neonatal connectome, the 68 regions of the adult connectome were manually overlapped with the regions provided in the Oishi atlas (Oishi et al. 2011)....
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...A neonate anatomical template (Oishi et al. 2011) was registered to the neonatal T1 image, and the 56 cortical regions of the template were selected as regions of interest....
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...Nodes were selected as the cortical regions of interest of the neonate template (Oishi et al. 2011), resulting in a parcellation of the whole neonate cerebral cortex into 56 regions (25 cortical regions covering each hemisphere, together with bilateral amygdala, hippocampus, and cerebellum)....
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...Image processing A neonate anatomical template (Oishi et al. 2011) was registered to the neonatal T1 image, and the 56 cortical regions of the template were selected as regions of interest....
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Book•DOI•

Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012

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Nicholas Ayache, Hervé Delingette, Polina Golland, Kensaku Mori

01 Jan 2012-Springer US

TL;DR: The model detected the enhanced segments with 91%/92% sensitivity/specificity which is better than the 81%/85% obtained by the voxel-independent approach and the clinical impact of the model in distinguishing between enhancing and nonenhancing ileum segments in 24 Crohn’s disease patients is demonstrated.

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Abstract: Diffusion-weighted MRI of the body has the potential to provide important new insights into physiological and microstructural properties. The Intra-Voxel Incoherent Motion (IVIM) model relates the observed DW-MRI signal decay to parameters that reflect perfusivity (D∗) and its volume fraction (f), and diffusivity (D). However, the commonly used voxel-wise fitting of the IVIM model leads to parameter estimates with poor precision, which has hampered their practical usage. In this work, we increase the estimates’ precision by introducing a model of spatial homogeneity, through which we obtain estimates of model parameters for all of the voxels at once, instead of solving for each voxel independently. Furthermore, we introduce an efficient iterative solver which utilizes a model-based bootstrap estimate of the distribution of residuals and a binary graph cut to generate optimal model parameter updates. Simulation experiments show that our approach reduces the relative root mean square error of the estimated parameters by 80% for the D∗ parameter and by 50% for the f and D parameters. We demonstrated the clinical impact of our model in distinguishing between enhancing and nonenhancing ileum segments in 24 Crohn’s disease patients. Our model detected the enhanced segments with 91%/92% sensitivity/specificity which is better than the 81%/85% obtained by the voxel-independent approach.

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251 citations

Cites background or methods from "Multi-contrast human neonatal brain..."

...331 Pew-Thian Yap and Dinggang Shen Tractography via the Ensemble Average Propagator in Diffusion MRI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339 Sylvain Merlet, Anne-Charlotte Philippe, Rachid Deriche, and Maxime Descoteaux Image Segmentation II A 4D Statistical Shape Model for Automated Segmentation of Lungs with Large Tumors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ....
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...247 Feng Shi, Li Wang, Guorong Wu, Yu Zhang, Manhua Liu, John H. Gilmore, Weili Lin, and Dinggang Shen Dictionary Learning and Time Sparsity in Dynamic MRI . . . . . . . . . . . . . 256 Jose Caballero, Daniel Rueckert, and Joseph V. Hajnal Joint Reconstruction of Image and Motion in MRI: Implicit Regularization Using an Adaptive 3D Mesh . . . . . . . . . . . . . . . . . . 264 Anne Menini, Pierre-André Vuissoz, Jacques Felblinger, and Freddy Odille Sparsity-Based Deconvolution of Low-Dose Perfusion CT Using Learned Dictionaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272 Ruogu Fang, Tsuhan Chen, and Pina C. Sanelli Fast Multi-contrast MRI Reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281 Junzhou Huang, Chen Chen, and Leon Axel Steady-State Model of the Radio-Pharmaceutical Uptake for MR-PET . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ....
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...MRI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 Matthew Toews, William M. Wells III, and Lilla Zöllei...
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...363 A. Kronman, Leo Joskowicz, and J. Sosna Segmentation of the Pectoral Muscle in Breast MRI Using Atlas-Based Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371 Albert Gubern-Mérida, Michiel Kallenberg, Robert Mart́ı, and Nico Karssemeijer Hierarchical Conditional Random Fields for Detection of Gad-Enhancing Lesions in Multiple Sclerosis . . . . . . . . . . . . . . . . . . . . . . . . 379 Zahra Karimaghaloo, Douglas L. Arnold, D. Louis Collins, and Tal Arbel XLII Table of Contents – Part II Simplified Labeling Process for Medical Image Segmentation . . . . . . . . . . 387 Mingchen Gao, Junzhou Huang, Xiaolei Huang, Shaoting Zhang, and Dimitris N. Metaxas Liver Segmentation Approach Using Graph Cuts and Iteratively Estimated Shape and Intensity Constrains . . . . . . . . . . . . . . . . . . . . . . . . . ....
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...Other groups have suggested incorporating spatial knowledge as a prior term to increase the reliability of parameters estimates in quantitative dynamic contrast enhanced MRI [6,10]....
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Journal Article•DOI•

Developmental Connectomics from Infancy through Early Childhood

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Miao Cao¹, Hao Huang², Yong He³, Yong He¹•Institutions (3)

McGovern Institute for Brain Research¹, Children's Hospital of Philadelphia², Beijing Normal University³

01 Aug 2017-Trends in Neurosciences

TL;DR: Five fundamental principles of brain network development during the critical first years of life are highlighted, emphasizing strengthened segregation/integration balance, a remarkable hierarchical order from primary to higher-order regions, unparalleled structural and functional maturations, substantial individual variability, and high vulnerability to risk factors and developmental disorders.

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182 citations

Cites background from "Multi-contrast human neonatal brain..."

...Because the brain changes rapidly during early development, age-specific templates should be constructed at high temporal resolution, such as gestational weeks or months, which remains challenging [95,96]....
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References

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Open Access

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Journal Article•DOI•

G*Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences

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Franz Faul¹, Edgar Erdfelder², Albert Georg Lang³, Axel Buchner³•Institutions (3)

University of Kiel¹, University of Mannheim², University of Düsseldorf³

01 May 2007-Behavior Research Methods

TL;DR: G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested.

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Abstract: G*Power (Erdfelder, Faul, & Buchner, 1996) was designed as a general stand-alone power analysis program for statistical tests commonly used in social and behavioral research. G*Power 3 is a major extension of, and improvement over, the previous versions. It runs on widely used computer platforms (i.e., Windows XP, Windows Vista, and Mac OS X 10.4) and covers many different statistical tests of thet, F, and χ2 test families. In addition, it includes power analyses forz tests and some exact tests. G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested. Like its predecessors, G*Power 3 is free.

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40,195 citations

"Multi-contrast human neonatal brain..." refers methods in this paper

...The software G*power (Faul et al., 2007) was used for the analysis....
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Book•

Co-planar stereotaxic atlas of the human brain : 3-dimensional proportional system : an approach to cerebral imaging

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J. Talairach, Pierre Tournoux, Mark Rayport

01 Jan 1988

TL;DR: Direct and Indirect Radiologic Localization Reference System: Basal Brain Line CA-CP Cerebral Structures in Three-Dimensional Space Practical Examples for the Use of the Atlas in Neuroradiologic Examinations Three- Dimensional Atlas of a Human Brain Nomenclature-Abbreviations Anatomic Index Conclusions.

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Abstract: Direct and Indirect Radiologic Localization Reference System: Basal Brain Line CA-CP Cerebral Structures in Three-Dimensional Space Practical Examples for the Use of the Atlas in Neuroradiologic Examinations Three-Dimensional Atlas of a Human Brain Nomenclature-Abbreviations Anatomic Index Conclusions.

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9,491 citations

Journal Article•DOI•

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M.J. Torrens

01 Mar 1990-Clinical Radiology

9,362 citations

"Multi-contrast human neonatal brain..." refers methods in this paper

..., 2009), based on Talairach’s atlas (Talairach and Tournoux, 1988)....
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...The nomenclature followed our previous adult MRI atlas (Oishi et al., 2009), based on Talairach’s atlas (Talairach and Tournoux, 1988)....
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Patent•DOI•

SENSE: Sensitivity Encoding for fast MRI

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Klaas P. Pruessmann¹, Markus Weiger¹, Markus B. Scheidegger¹, Peter Boesiger¹•Institutions (1)

ETH Zurich¹

14 Apr 1999-Magnetic Resonance in Medicine

TL;DR: The problem of image reconstruction from sensitivity encoded data is formulated in a general fashion and solved for arbitrary coil configurations and k‐space sampling patterns and special attention is given to the currently most practical case, namely, sampling a common Cartesian grid with reduced density.

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Abstract: The invention relates to a method of parallel imaging for obtaining images by means of magnetic resonance (MR). The method includes the simultaneous measurement of sets of MR singals by an array of receiver coils, and the reconstruction of individual receiver coil images from the sets of MR signals. In order to reduce the acquisition time, the distance between adjacent phase encoding lines in k-space is increased, compared to standard Fourier imaging, by a non-integer factor smaller than the number of receiver coils. This undersampling gives rise to aliasing artifacts in the individual receiver coil images. An unaliased final image with the same field of view as in standard Fourier imaging is formed from a combination of the individual receiver coil images whereby account is taken of the mutually different spatial sensitivities of the receiver coils at the positions of voxels which in the receiver coil images become superimposed by aliasing. This requires the solution of a linear equation by means of the generalised inverse of a sensitivity matrix. The reduction of the number of phase encoding lines by a non-integer factor compared to standard Fourier imaging provides that different numbers of voxels become superimposed (by aliasing) in different regions of the receiver coil images. This effect can be exploited to shift residual aliasing artifacts outside the area of interest.

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6,562 citations

"Multi-contrast human neonatal brain..." refers methods in this paper

...A single-shot EPI with SENSE acquisition was used for DTI (Bammer et al., 2001; Jaermann et al., 2004; Pruessmann et al., 1999)....
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Journal Article•DOI•

The basis of anisotropic water diffusion in the nervous system – a technical review

[...]

Christian Beaulieu¹•Institutions (1)

University of Alberta¹

01 Nov 2002-NMR in Biomedicine

TL;DR: The purpose of this review is to characterize the relationship of nuclear magnetic resonance measurements of water diffusion and its anisotropy (i.e. directional dependence) with the underlying microstructure of neural fibres.

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Abstract: Anisotropic water diffusion in neural fibres such as nerve, white matter in spinal cord, or white matter in brain forms the basis for the utilization of diffusion tensor imaging (DTI) to track fibre pathways. The fact that water diffusion is sensitive to the underlying tissue microstructure provides a unique method of assessing the orientation and integrity of these neural fibres, which may be useful in assessing a number of neurological disorders. The purpose of this review is to characterize the relationship of nuclear magnetic resonance measurements of water diffusion and its anisotropy (i.e. directional dependence) with the underlying microstructure of neural fibres. The emphasis of the review will be on model neurological systems both in vitro and in vivo. A systematic discussion of the possible sources of anisotropy and their evaluation will be presented followed by an overview of various studies of restricted diffusion and compartmentation as they relate to anisotropy. Pertinent pathological models, developmental studies and theoretical analyses provide further insight into the basis of anisotropic diffusion and its potential utility in the nervous system.

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4,216 citations

"Multi-contrast human neonatal brain..." refers background in this paper

...In addition, DTI can provide quantitative measures related to water diffusivity, which is believed to reflect certain maturation processes, such as axonal growth and myelination (Beaulieu, 2002; Dubois et al., 2008; Mori and Zhang, 2006; Mukherjee et al., 2002; Ramenghi et al., 2009)....
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