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Fetal MRI by robust deep generative prior reconstruction and diffeomorphic registration: application to gestational age prediction [article]

Lucilio Cordero-Grande, Juan Enrique Ortuño-Fisac, Alena Uus, Maria Deprez, Andrés Santos, Joseph V. Hajnal, María Jesús Ledesma-Carbayo
2021 arXiv   pre-print
Thus, in this paper we propose a deep generative prior for robust volumetric reconstructions integrated with a diffeomorphic volume to slice registration method.  ...  Results suggest improved image resolution and more accurate prediction of gestational age at scan when comparing to a state of the art reconstruction method.  ...  Acknowledgments This work is funded by the Ministry of Science and Innovation, Spain, under the Beatriz Galindo Programme [BGP18/00178].  ... 
arXiv:2111.00102v1 fatcat:jo47swcc2jbzvpju56thhprwqe

Real-time Deep Pose Estimation with Geodesic Loss for Image-to-Template Rigid Registration [article]

Seyed Sadegh Mohseni Salehi, Shadab Khan, Deniz Erdogmus, Ali Gholipour
2018 arXiv   pre-print
We trained our models on T2-weighted fetal brain MRI scans and used them to predict the 3D pose of newborn brains based on T1-weighted MRI scans.  ...  With an aim to increase the capture range and accelerate the performance of state-of-the-art inter-subject and subject-to-template 3D registration, we propose deep learning-based methods that are trained  ...  [27] used slice-to-volume registration for fetal brain MRI reconstruction.  ... 
arXiv:1803.05982v4 fatcat:xglh3t66vfdznnyscnc72chfzq

Real-time Deep Pose Estimation with Geodesic Loss for Image-to-Template Rigid Registration

2018 IEEE Transactions on Medical Imaging  
We trained our models on T2-weighted fetal brain MRI scans and used them to predict the 3-D pose of newborn brains based on T1-weighted MRI scans.  ...  As an exemplary application, we applied the proposed methods to register arbitrarily oriented reconstructed images of fetuses scanned in-utero at a wide gestational age range to a standard atlas space.  ...  Acknowledgments This study was supported in part by the McKnight Foundation through a Technological Innovations in Neuroscience Award, and in part by the National Institute of Biomedical Imaging and Bioengineering  ... 
doi:10.1109/tmi.2018.2866442 pmid:30138909 pmcid:PMC6438698 fatcat:qwrblvzmbvf77aat7pg5dle2vq

A Deep Attentive Convolutional Neural Network for Automatic Cortical Plate Segmentation in Fetal MRI [article]

Haoran Dou, Davood Karimi, Caitlin K. Rollins, Cynthia M. Ortinau, Lana Vasung, Clemente Velasco-Annis, Abdelhakim Ouaalam, Xin Yang, Dong Ni, Ali Gholipour
2021 arXiv   pre-print
in the gestational age range of 16 to 39 weeks.  ...  Automatic segmentation of the cortical plate, on the other hand, is challenged by the relatively low resolution of the reconstructed fetal brain MRI scans compared to the thin structure of the cortical  ...  Fetal MRI data The fetal MRI dataset used in this study consisted of superresolution reconstructed volumes of 57 fetuses scanned at a gestational age (GA) between 16 and 39 weeks (29.5±5.5).  ... 
arXiv:2004.12847v3 fatcat:r26i6yn4tnhhrn66ld2kfnrp6m

A discriminative feature selection approach for shape analysis: Application to fetal brain cortical folding

J. Pontabry, F. Rousseau, C. Studholme, M. Koob, J.-L. Dietemann
2017 Medical Image Analysis  
The development of post-processing reconstruction techniques has opened new possibilities for the study of in-utero fetal brain MRI data.  ...  The proposed method is used to sparsely characterize cortical folding patterns of an in-utero fetal MR dataset, labeled with heterogeneous gestational age ranging from 26 weeks to 34 weeks.  ...  This work is also funded by NIH Grant R01 NS055064 and R01 EB017133. J. P. was partially supported through the ERC-Stg "NuclearPotency" granted to M. E. Torres-Padilla.  ... 
doi:10.1016/ pmid:27498089 pmcid:PMC5501094 fatcat:lmeqbneqhfhonjpduwpyiocyne

Front Matter: Volume 11596

Bennett A. Landman, Ivana Išgum
2021 Medical Imaging 2021: Image Processing  
The papers in this volume were part of the technical conference cited on the cover and title page. Papers were selected and subject to review by the editors and conference program committee.  ...  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.  ...  1160211596 1NAn automated framework for image classification and segmentation of fetal ultrasound images for gestational age estimation 11596 1O Assessing the generalizability of temporally coherent echocardiography  ... 
doi:10.1117/12.2595437 fatcat:7x4u3yicqvev5n3gmo54gqr2am

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.  ...  However, infant brain MR images typically exhibit reduced tissue contrast (especially around 6 months of age), large within-tissue intensity variations, and regionally-heterogeneous, dynamic changes, in  ...  Acknowledgements This work was partially supported by NIH grants (MH100217, MH107815, MH108914, MH109773, MH110274 and NS093842).  ... 
doi:10.1016/j.neuroimage.2018.03.042 pmid:29574033 pmcid:PMC6150852 fatcat:w2o27wt5afhktd7zoophmhnmi4

Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: a review [article]

Fan Zhang, Alessandro Daducci, Yong He, Simona Schiavi, Caio Seguin, Robert Smith, Chun-Hung Yeh, Tengda Zhao, Lauren J. O'Donnell
2021 arXiv   pre-print
We then review studies that have used quantitative tractography approaches to study the brain's white matter, focusing on applications in neurodevelopment, aging, neurological disorders, mental disorders  ...  For each step, we aim to describe methodological choices, their popularity, and potential pros and cons.  ...  CHY is grateful to the Ministry of Science and Technology of Taiwan (MOST 109-2222-E-182-001-MY3) for the support.  ... 
arXiv:2104.11644v1 fatcat:l3ixpcwu7jb7zcqo2sm5pswmja

Scientific Exhibits

2014 Journal of Medical Radiation Sciences  
The outcome of this study will lead to VMAT playing a vital role in the management of MPM, by reducing dose toxicity to OARs, increasing dose conformity to the PTV and reducing overall treatment times.  ...  All patients were simulated with CT and MRI before and after injection of 10 cc of Hydrogel. The first 10 patients had an additional MRI at completion of radiation.  ...  Bone detail was excellent in all fetuses, regardless of gestational age. There was good correlation between imaging and autopsy measurements of fetal and organ size.  ... 
doi:10.1002/jmrs.74 pmid:27759942 pmcid:PMC4263487 fatcat:ccsk62gef5g47bfugrvtwqapj4

Quantification of cortical folding using MR image data

Robert Wright, Daniel Rueckert, Paul Aljabar, Engineering And Physical Sciences Research Council
The changing relationship between the folding measures and gestational age was modelled with a Gompertz function which allowed an accurate prediction of physiological age.  ...  This methodology was applied to fetuses over a wide gestational age range (21.7 to 38.9 weeks) for a large number of subjects (N = 80) extending our understanding of how the cortex folds through this critical  ...  Gestational age was predicted from the observed value of H N by taking the inverse of the Gompertz function fitted to the data for H N .  ... 
doi:10.25560/39037 fatcat:zmqceawl2nh6bj55spmlctnq2y

Introduction to JINS Special Issue on Human Brain Connectivity in the Modern Era: Relevance to Understanding Health and Disease

Deanna M. Barch, Mieke Verfaellie, Stephen M. Rao
2016 Journal of the International Neuropsychological Society  
Janes and Stern share co-last authorship. ACKNOWLEDGMENTS There are no competing interests to declare for all authors. This work was supported by the BRAINS RO1 (to S.A.L.; MH 091811).  ...  The first author gratefully acknowledges the training and mentoring provided by Drs. Edith Kaplan and Norman Geschwind.  ...  MRI Predictors of Prognosis Another potentially important application of longitudinal MRI is the prediction of prognosis (i.e., to predict later behavioral and functional outcomes).  ... 
doi:10.1017/s1355617716000047 fatcat:f2preenihbes5ftkrxbo7tgt64

Longitudinal diffeomorphic fetal brain atlas learning for tissue labeling using geodesic regression and graph cuts

Roxane Licandro, Robert Sablatnig, Georg Langs
It allows to image a fetus within 20 seconds and consequently reduce artefacts, caused by the fetal movement. A problem of MR imaging is the lack of comparability and constancy of gray-values.  ...  The fetal atlas building process takes into account both inter-patient variability of brain shapes and the gestational age dependent structural changes. Thus, a time-varying atlas is required.  ...  [33] construct a time-varying fetal brain atlas with application on segmentation. The gestational age ranges from 20.57 to 24.71 GWs.  ... 
doi:10.34726/hss.2015.21890 fatcat:6rhduuyexjct3cuybbbm7acuvi

Computational models of the morphology of the developing neonatal human brain

Andreas Schuh, Daniel Rueckert
Our models were found by experts to be superior to the original segmentation in terms of accurately delineating t [...]  ...  We evaluate approaches for the fast diffeomorphic registration on a publicly available neonatal brain image dataset, and present an improved inverse consistent variant of the stationary velocity free-form  ...  Acknowledgements It has been a long journey leading up to this work, starting with the guidance, opportunities, and encouragement I have received from advisors before starting the Ph.  ... 
doi:10.25560/58880 fatcat:247gouybmzajbpic2ryusmwdiu

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

Hui Xue, Jo Hajnal, Daniel Rueckert
The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching.  ...  To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed.  ...  In the future we would like to apply this type of registration technique to both fetal and neonatal brains at different gestational ages in order to develop atlases of normal cortical growth patterns so  ... 
doi:10.25560/1373 fatcat:d3m3lijkongc3majjsmz4jy5ya

Poster Session II

2010 Neuropsychopharmacology  
Data Analysis: FSL provided the tools for preprocessing, registration, and analysis. We modeled the responses to stimuli using the general linear model.  ...  to this robust interaction.  ...  to rats prior to performance of the light/dark (LD), test for anxiety to probe age differences in serotonergic function.  ... 
doi:10.1038/npp.2010.217 fatcat:gbcgyi35jbdndlwhlgwio7ts7y
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