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Temporally-Consistent Surface Reconstruction using Metrically-Consistent Atlases [article]

Jan Bednarik, Noam Aigerman, Vladimir G. Kim, Siddhartha Chaudhuri, Shaifali Parashar, Mathieu Salzmann, Pascal Fua
2021 arXiv   pre-print
We propose a method for unsupervised reconstruction of a temporally-consistent sequence of surfaces from a sequence of time-evolving point clouds.  ...  We represent the reconstructed surfaces as atlases computed by a neural network, which enables us to establish correspondences between frames.  ...  Left: The reconstructed surfaces, textured with a consistent texture to exhibit the temporally-consistent correspondences between the surfaces.  ... 
arXiv:2111.06838v1 fatcat:qxpkltoanbepxdhnw2e2zgegsa

Temporally-Coherent Surface Reconstruction via Metric-Consistent Atlases [article]

Jan Bednarik, Vladimir G. Kim, Siddhartha Chaudhuri, Shaifali Parashar, Mathieu Salzmann, Pascal Fua, Noam Aigerman
2021 arXiv   pre-print
We represent the reconstructed surface as an atlas, using a neural network.  ...  We propose a method for the unsupervised reconstruction of a temporally-coherent sequence of surfaces from a sequence of time-evolving point clouds, yielding dense, semantically meaningful correspondences  ...  Temporally-coherent surface reconstruction Atlases via a neural network.  ... 
arXiv:2104.06950v2 fatcat:llkobvl4rjcllohrufvdr5rke4

Myelo- and cytoarchitectonic microstructural and functional human cortical atlases reconstructed in common MRI space

Rory Pijnenburg, Lianne H. Scholtens, Dirk Jan Ardesch, Siemon C. de Lange, Yongbin Wei, Martijn P. van den Heuvel
2021 NeuroImage  
Digital reconstructions of these important cortical atlases widen the range of modalities for which cortex-wide imaging atlases are currently available and offer the opportunity to compare and combine  ...  The parcellation of the brain's cortical surface into anatomically and/or functionally distinct areas is a topic of ongoing investigation and interest.  ...  This asymmetric consistency metric is a variant of the intersection over union metric and has the benefit that it is also suitable for comparing atlases in which cortical regions differ in size between  ... 
doi:10.1016/j.neuroimage.2021.118274 pmid:34146709 fatcat:rgvuyoyhgjdtrjnv7venwiir5e

Construction of 4D high-definition cortical surface atlases of infants: Methods and applications

Gang Li, Li Wang, Feng Shi, John H. Gilmore, Weili Lin, Dinggang Shen
2015 Medical Image Analysis  
surfaces across infant individuals, in comparison to the infant surface atlases constructed without longitudinal consistency and also the FreeSurfer adult surface atlas.  ...  Experimental results on two independent infant MRI datasets show that using our 4D infant cortical surface atlases as templates leads to significantly improved accuracy for spatial normalization of cortical  ...  consistency by 4D infant surface atlases.  ... 
doi:10.1016/j.media.2015.04.005 pmid:25980388 pmcid:PMC4540689 fatcat:5hbvho55i5aolld4bdcofhfzzu

Age-specific Structural Fetal Brain Atlases Construction and Cortical Development Quantification for Chinese Population

Jiangjie Wu, Taotao Sun, Boliang Yu, Zhenghao Li, Qing Wu, Yutong Wang, Zhaoxia Qian, Yuyao Zhang, Ling Jiang, Hongjiang Wei
2021 NeuroImage  
Additionally, a direct comparison of the Chinese fetal atlases and Caucasian fetal atlases reveals dramatic anatomical differences, mainly in the medial frontal and temporal regions.  ...  In this paper, we use an unbiased template construction algorithm to create a set of age-specific Chinese fetal atlases between 21-35 weeks of gestation from 115 normal fetal brains.  ...  In our study, the fetal brains were reconstructed using the 3D voxel-wise super-resolution reconstruction, and the weekly gestation-age-specific anatomical fetal brain atlases are generated from 22w to  ... 
doi:10.1016/j.neuroimage.2021.118412 pmid:34298085 fatcat:qntt24vjq5gztgncw6vckbw6yq

Joint prediction of longitudinal development of cortical surfaces and white matter fibers from neonatal MRI

Islem Rekik, Gang Li, Pew-Thian Yap, Geng Chen, Weili Lin, Dinggang Shen
2017 NeuroImage  
Second, for temporally consistent fiber prediction, we propose to reliably estimate connectivity features using low-rank tensor completion, thereby capturing the variability and richness of the temporal  ...  First, for a more accurate cortical surface prediction, instead of simply relying on one neonatal atlas to guide the prediction of the multishape, we propose to use multiple neonatal atlases to build a  ...  Cortical surface reconstruction. For each segmented image, we reconstructed the inner cortical surface for each hemisphere using a deformable surface method .  ... 
doi:10.1016/j.neuroimage.2017.03.012 pmid:28284800 pmcid:PMC5432411 fatcat:pxk6gs3fifhfxgto6l7voc4rda

Probabilistic Maps of Visual Topography in Human Cortex

Liang Wang, Ryan E.B. Mruczek, Michael J. Arcaro, Sabine Kastner
2014 Cerebral Cortex  
Using standard fMRI paradigms, we identified 25 topographic maps in a large population of individual subjects (N = 53) and transformed them into either a surface-or volume-based standardized space.  ...  Overall, the probabilistic atlases quantify the variability of topographic representations in human cortex and provide a useful reference for comparing data across studies that can be transformed into  ...  Surface Reconstruction For each subject, 2 high-resolution structural scans (MPRAGE, same parameters as above) were acquired in one of the scanning sessions, averaged, and used for cortical surface reconstruction  ... 
doi:10.1093/cercor/bhu277 pmid:25452571 pmcid:PMC4585523 fatcat:lz7ucmhtnnevxj7eiw2kotr7wa

Mapping Region-Specific Longitudinal Cortical Surface Expansion from Birth to 2 Years of Age

G. Li, J. Nie, L. Wang, F. Shi, W. Lin, J. H. Gilmore, D. Shen
2012 Cerebral Cortex  
On the basis of the surface-based atlases, we study the longitudinal cortical surface expansion in the first 2 years of life and find that cortical surface expansion is age related and region specific.  ...  In this article, we generate the first longitudinal surface-based atlases of human cortical structures at 0, 1, and 2 years of age from 73 healthy subjects.  ...  Figure 1 . 1 Illustration of cortical surface reconstruction and longitudinal surface-based atlases generation.  ... 
doi:10.1093/cercor/bhs265 pmid:22923087 pmcid:PMC3792744 fatcat:i4rgdzkqgnec5ed4u7ptppxzyq

A spatio-temporal atlas and statistical model of the tongue during speech from cine-MRI

Jonghye Woo, Fangxu Xing, Junghoon Lee, Maureen Stone, Jerry L. Prince
2016 Computer Methods in Biomechanics and Biomedical Engineering Imaging & Visualization  
The model is based on the cine-MRI from twenty two normal speakers and consists of several steps involving both spatial and temporal alignment problems independently.  ...  Finally, the spatio-temporal atlas is created by time-warping each subject, generating new mean images at each time, and producing shape statistics around these mean images using principal component analysis  ...  In this work, we use CC as our similarity metric.  ... 
doi:10.1080/21681163.2016.1169220 pmid:30034953 pmcid:PMC6051546 fatcat:6a7idepcmzhhnjdklnzpkmryja

Consistent cortical reconstruction and multi-atlas brain segmentation

Yuankai Huo, Andrew J. Plassard, Aaron Carass, Susan M. Resnick, Dzung L. Pham, Jerry L. Prince, Bennett A. Landman
2016 NeuroImage  
FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces.  ...  Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain.  ...  This study was also supported by NIH 5R01NS056307, 5R21NS082891 and in part using the resources of the Advanced Computing Center for Research and Education  ... 
doi:10.1016/j.neuroimage.2016.05.030 pmid:27184203 pmcid:PMC4927397 fatcat:aagizrwmujaktlmfkp7atpou2i

Computational neuroanatomy of baby brains: A review

Gang Li, Li Wang, Pew-Thian Yap, Fan Wang, Zhengwang Wu, Yu Meng, Pei Dong, Jaeil Kim, Feng Shi, Islem Rekik, Weili Lin, Dinggang Shen
2018 NeuroImage  
We also summarize publically available infant-dedicated resources, including MRI datasets, computational tools, grand challenges, and brain atlases.  ...  When removing the temporal constraint, this method can also be used to reconstruct infant cortical surfaces at a single time point.  ...  for temporally-consistent labeling of longitudinal infant images.  ... 
doi:10.1016/j.neuroimage.2018.03.042 pmid:29574033 pmcid:PMC6150852 fatcat:w2o27wt5afhktd7zoophmhnmi4

Conserved and variable architecture of human white matter connectivity

Danielle S. Bassett, Jesse A. Brown, Vibhas Deshpande, Jean M. Carlson, Scott T. Grafton
2011 NeuroImage  
Basic connectivity properties and several graph metrics consistently displayed high reproducibility and low variability in both DSI and DTI networks.  ...  Deterministic tractography was performed on each dataset and inter-regional connectivity matrices were then derived by applying each of three widely used whole-brain parcellation schemes over a range of  ...  The voxel-based tract reconstruction was then parcellated using a variety of templates including 3 whole-brain atlases (AAL, HO, and LPBA40) and iteratively upsampled versions of these atlases: Sub 1 containing  ... 
doi:10.1016/j.neuroimage.2010.09.006 pmid:20850551 fatcat:t74urb263ja4zap4wnue4uhmny

Finite Element Decomposition of Human Neocortex [chapter]

David A. Batte, Travis S. Chow, Bruce H. McCormick
1998 Computational Neuroscience  
The decomposition satisfies neuroanatomical consistency, a set of constraints defined by neuroanatomists' needs, the anatomical structure of the brain, and the positioning of neurons inside the neocortical  ...  The Reconstruction Process The surface reconstruction process consists of five stages.  ...  Most of the existent surfacebased atlases model the brain with polyhedral surfaces constructed using serial surface reconstruction or conversion algorithms applied to the voxel datasets, e.g. the wrapper  ... 
doi:10.1007/978-1-4615-4831-7_95 fatcat:rjafsifzmng2xb2mbv2mpyifdy

Multifaceted Atlases of the Human Brain in its Infancy [article]

Sahar Ahmad, Ye Wu, Zhengwang Wu, Kim-Han Thung, Weili Lin, Gang Li, Li Wang, Pew-Thian Yap
2022 bioRxiv   pre-print
Here, we introduce for the first time a collection of atlases that charts postnatal development of the human brain in a spatio-temporally dense manner from two weeks to two years of age.  ...  Existing surface and volumetric atlases are typically constructed independently in different coordinate spaces, causing discrepancies and complications in multifaceted analyses.  ...  reconstruction 100, 101 .  ... 
doi:10.1101/2022.03.19.484985 fatcat:7xsgtyykkbhf3okqbla4bupv34

An automatic pipeline for atlas-based fetal and neonatal brain segmentation and analysis [article]

Urru, Andrea and Nakaki, Ayako and Benkarim, Oualid and Crovetto, Francesca and Segales, Laura and Comte, Valentin and Hahner, Nadine and Eixarch, Elisenda and Gratacós, Eduard and Crispi, Fàtima and Piella, Gemma and González Ballester (+1 others)
2022 arXiv   pre-print
We also report the creation of two new fetal atlases, and their use within the pipeline for atlas-based segmentation, based on novel registration methods.  ...  The pipeline is also able to extract cortical and pial surfaces and compute features, such as curvature, thickness, sulcal depth, and local gyrification index.  ...  The tissue priors for gray matter and ventricles are computed registering the obtained T2-weighted reconstructed image to the temporal templates, and they are used with the T2 image in a 3-channel registration  ... 
arXiv:2205.07575v1 fatcat:riyk2obv45ahnks6y6jicjva5e
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