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Calixto C, Taymourtash A, Karimi D, Snoussi H, Velasco-Annis C, Jaimes C, Gholipour A. Advances in Fetal Brain Imaging. Magn Reson Imaging Clin N Am 2024; 32:459-478. [PMID: 38944434 PMCID: PMC11216711 DOI: 10.1016/j.mric.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2024]
Abstract
Over the last 20 years, there have been remarkable developments in fetal brain MR imaging analysis methods. This article delves into the specifics of structural imaging, diffusion imaging, functional MR imaging, and spectroscopy, highlighting the latest advancements in motion correction, fetal brain development atlases, and the challenges and innovations. Furthermore, this article explores the clinical applications of these advanced imaging techniques in comprehending and diagnosing fetal brain development and abnormalities.
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Affiliation(s)
- Camilo Calixto
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, 401 Park Dr, 7th Floor West, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.
| | - Athena Taymourtash
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Spitalgasse 23, Wien 1090, Austria
| | - Davood Karimi
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, 401 Park Dr, 7th Floor West, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Haykel Snoussi
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, 401 Park Dr, 7th Floor West, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Clemente Velasco-Annis
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, 401 Park Dr, 7th Floor West, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Camilo Jaimes
- Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Department of Radiology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02215, USA
| | - Ali Gholipour
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital, 401 Park Dr, 7th Floor West, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
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Zhao L, Zhu D, Wang X, Liu X, Li T, Wang B, Yao Z, Zheng W, Hu B. An Attention-Based Hemispheric Relation Inference Network for Perinatal Brain Age Prediction. IEEE J Biomed Health Inform 2024; 28:4483-4493. [PMID: 38857141 DOI: 10.1109/jbhi.2024.3411620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Brain anatomical age is an effective feature to assess the status of the brain, such as atypical development and aging. Although some deep learning models have been developed for estimating infant brain age, the performance of these models was unsatisfactory because few of them considered the developmental characteristics of brain anatomy during the perinatal period-the most rapid and complex developmental stage across the lifespan. The present study proposed an attention-based hemispheric relation inference network (HRINet) that takes advantage of the nature of brain structural lateralization during early development. This model captures the inter-hemispheric relationship using a graph attention mechanism and transmits lateralization information as features to describe the interactive development between bilateral hemispheres. The HRINet was used to estimate the brain age of 531 preterm and full-term neonates from the Developing Human Connectome Project (dHCP) database based on two metrics (mean curvature and sulcal depth) characterizing the folding morphology of the cortex. Our results showed that the HRINet outperformed other benchmark models in fitting the perinatal brain age, with mean absolute error of 0.53 and determination coefficient of 0.89. We also verified the generalizability of the HRINet on an extra independent dataset collected from the Gansu Provincial Maternity and Child-care Hospital. Furthermore, by applying the best-performing model to an independent dataset consisting of 47 scans of preterm infants at term-equivalent age, we showed that the predicted age was significantly lower than the chronological age, suggesting a delayed development of premature brains. Our results demonstrate the effectiveness and generalizability of the HRINet in estimating infant brain age, providing promising clinical applications for assessing neonatal brain maturity.
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Sheng Y, Wang Y, Wang X, Zhang Z, Zhu D, Zheng W. No sex difference in maturation of brain morphology during the perinatal period. Brain Struct Funct 2024:10.1007/s00429-024-02828-x. [PMID: 39020216 DOI: 10.1007/s00429-024-02828-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024]
Abstract
Accumulating evidence have documented sex differences in brain anatomy from early childhood to late adulthood. However, whether sex difference of brain structure emerges in the neonatal brain and how sex modulates the development of cortical morphology during the perinatal stage remains unclear. Here, we utilized T2-weighted MRI from the Developing Human Connectome Project (dHCP) database, consisting of 41 male and 40 female neonates born between 35 and 43 postmenstrual weeks (PMW). Neonates of each sex were arranged in a continuous ascending order of age to capture the progressive changes in cortical thickness and curvature throughout the developmental continuum. The maturational covariance network (MCN) was defined as the coupled developmental fluctuations of morphology measures between cortical regions. We constructed MCNs based on the two features, respectively, to illustrate their developmental interdependencies, and then compared the network topology between sexes. Our results showed that cortical structural development exhibited a localized pattern in both males and females, with no significant sex differences in the developmental trajectory of cortical morphology, overall organization, nodal importance, and modular structure of the MCN. Furthermore, by merging male and female neonates into a unified cohort, we identified evident dependencies influences in structural development between different brain modules using the Granger causality analysis (GCA), emanating from high-order regions toward primary cortices. Our findings demonstrate that the maturational pattern of cortical morphology may not differ between sexes during the perinatal period, and provide evidence for the developmental causality among cortical structures in perinatal brains.
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Affiliation(s)
- Yucen Sheng
- School of Foreign Languages, Lanzhou Jiaotong University, Lanzhou, People's Republic of China
| | - Ying Wang
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, People's Republic of China
| | - Xiaomin Wang
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, People's Republic of China
| | - Zhe Zhang
- Institute of Brain Science, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Dalin Zhu
- Department of Medical Imaging Center, Gansu Provincial Maternity and Child-Care Hospital Lanzhou, Lanzhou, People's Republic of China.
| | - Weihao Zheng
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, People's Republic of China.
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Wang Y, Zhu D, Zhao L, Wang X, Zhang Z, Hu B, Wu D, Zheng W. Profiling cortical morphometric similarity in perinatal brains: Insights from development, sex difference, and inter-individual variation. Neuroimage 2024; 295:120660. [PMID: 38815676 DOI: 10.1016/j.neuroimage.2024.120660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
The topological organization of the macroscopic cortical networks important for the development of complex brain functions. However, how the cortical morphometric organization develops during the third trimester and whether it demonstrates sexual and individual differences at this particular stage remain unclear. Here, we constructed the morphometric similarity network (MSN) based on morphological and microstructural features derived from multimodal MRI of two independent cohorts (cross-sectional and longitudinal) scanned at 30-44 postmenstrual weeks (PMW). Sex difference and inter-individual variations of the MSN were also examined on these cohorts. The cross-sectional analysis revealed that both network integration and segregation changed in a nonlinear biphasic trajectory, which was supported by the results obtained from longitudinal analysis. The community structure showed remarkable consistency between bilateral hemispheres and maintained stability across PMWs. Connectivity within the primary cortex strengthened faster than that within high-order communities. Compared to females, male neonates showed a significant reduction in the participation coefficient within prefrontal and parietal cortices, while their overall network organization and community architecture remained comparable. Furthermore, by using the morphometric similarity as features, we achieved over 65 % accuracy in identifying an individual at term-equivalent age from images acquired after birth, and vice versa. These findings provide comprehensive insights into the development of morphometric similarity throughout the perinatal cortex, enhancing our understanding of the establishment of neuroanatomical organization during early life.
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Affiliation(s)
- Ying Wang
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Dalin Zhu
- Department of Medical Imaging Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Leilei Zhao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Xiaomin Wang
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
| | - Zhe Zhang
- Institute of Brain Science, Hangzhou Normal University, Hangzhou, China; School of Physics, Hangzhou Normal University, Hangzhou, China
| | - Bin Hu
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China; School of Medical Technology, Beijing Institute of Technology, Beijing, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.
| | - Weihao Zheng
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China.
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Calixto C, Machado-Rivas F, Karimi D, Velasco C, Cortes-Albornoz MC, Afacan O, Warfield SK, Gholipour A, Jaimes C. Population Atlas Analysis of Emerging Brain Structural Connections in the Human Fetus. J Magn Reson Imaging 2024; 60:152-160. [PMID: 37842932 PMCID: PMC11018715 DOI: 10.1002/jmri.29057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
BACKGROUND A lack of in utero imaging data hampers our understanding of the connections in the human fetal brain. Generalizing observations from postmortem subjects and premature newborns is inaccurate due to technical and biological differences. PURPOSE To evaluate changes in fetal brain structural connectivity between 23 and 35 weeks postconceptional age using a spatiotemporal atlas of diffusion tensor imaging (DTI). STUDY TYPE Retrospective. POPULATION Publicly available diffusion atlases, based on 60 healthy women (age 18-45 years) with normal prenatal care, from 23 and 35 weeks of gestation. FIELD STRENGTH/SEQUENCE 3.0 Tesla/DTI acquired with diffusion-weighted echo planar imaging (EPI). ASSESSMENT We performed whole-brain fiber tractography from DTI images. The cortical plate of each diffusion atlas was segmented and parcellated into 78 regions derived from the Edinburgh Neonatal Atlas (ENA33). Connectivity matrices were computed, representing normalized fiber connections between nodes. We examined the relationship between global efficiency (GE), local efficiency (LE), small-worldness (SW), nodal efficiency (NE), and betweenness centrality (BC) with gestational age (GA) and with laterality. STATISTICAL TESTS Linear regression was used to analyze changes in GE, LE, NE, and BC throughout gestation, and to assess changes in laterality. The t-tests were used to assess SW. P-values were corrected using Holm-Bonferroni method. A corrected P-value <0.05 was considered statistically significant. RESULTS Network analysis revealed a significant weekly increase in GE (5.83%/week, 95% CI 4.32-7.37), LE (5.43%/week, 95% CI 3.63-7.25), and presence of SW across GA. No significant hemisphere differences were found in GE (P = 0.971) or LE (P = 0.458). Increasing GA was significantly associated with increasing NE in 41 nodes, increasing BC in 3 nodes, and decreasing BC in 2 nodes. DATA CONCLUSION Extensive network development and refinement occur in the second and third trimesters, marked by a rapid increase in global integration and local segregation. LEVEL OF EVIDENCE 3 TECHNICAL EFFICACY: Stage 2.
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Affiliation(s)
- Camilo Calixto
- Computational Radiology Laboratory. Department of Radiology. Boston Children’s Hospital. Boston, MA
- Harvard Medical School. Boston, MA
| | - Fedel Machado-Rivas
- Harvard Medical School. Boston, MA
- Massachusetts General Hospital. Boston, MA
| | - Davood Karimi
- Computational Radiology Laboratory. Department of Radiology. Boston Children’s Hospital. Boston, MA
- Harvard Medical School. Boston, MA
| | - Clemente Velasco
- Computational Radiology Laboratory. Department of Radiology. Boston Children’s Hospital. Boston, MA
- Harvard Medical School. Boston, MA
| | | | - Onur Afacan
- Computational Radiology Laboratory. Department of Radiology. Boston Children’s Hospital. Boston, MA
- Harvard Medical School. Boston, MA
| | - Simon K. Warfield
- Computational Radiology Laboratory. Department of Radiology. Boston Children’s Hospital. Boston, MA
- Harvard Medical School. Boston, MA
| | - Ali Gholipour
- Computational Radiology Laboratory. Department of Radiology. Boston Children’s Hospital. Boston, MA
- Harvard Medical School. Boston, MA
| | - Camilo Jaimes
- Harvard Medical School. Boston, MA
- Massachusetts General Hospital. Boston, MA
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Kebiri H, Gholipour A, Lin R, Vasung L, Calixto C, Krsnik Ž, Karimi D, Bach Cuadra M. Deep learning microstructure estimation of developing brains from diffusion MRI: A newborn and fetal study. Med Image Anal 2024; 95:103186. [PMID: 38701657 DOI: 10.1016/j.media.2024.103186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/06/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024]
Abstract
Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. Fiber orientation distribution functions (FODs) are a common way of representing the orientation and density of white matter fibers. However, with standard FOD computation methods, accurate estimation requires a large number of measurements that usually cannot be acquired for newborns and fetuses. We propose to overcome this limitation by using a deep learning method to map as few as six diffusion-weighted measurements to the target FOD. To train the model, we use the FODs computed using multi-shell high angular resolution measurements as target. Extensive quantitative evaluations show that the new deep learning method, using significantly fewer measurements, achieves comparable or superior results than standard methods such as Constrained Spherical Deconvolution and two state-of-the-art deep learning methods. For voxels with one and two fibers, respectively, our method shows an agreement rate in terms of the number of fibers of 77.5% and 22.2%, which is 3% and 5.4% higher than other deep learning methods, and an angular error of 10° and 20°, which is 6° and 5° lower than other deep learning methods. To determine baselines for assessing the performance of our method, we compute agreement metrics using densely sampled newborn data. Moreover, we demonstrate the generalizability of the new deep learning method across scanners, acquisition protocols, and anatomy on two clinical external datasets of newborns and fetuses. We validate fetal FODs, successfully estimated for the first time with deep learning, using post-mortem histological data. Our results show the advantage of deep learning in computing the fiber orientation density for the developing brain from in-vivo dMRI measurements that are often very limited due to constrained acquisition times. Our findings also highlight the intrinsic limitations of dMRI for probing the developing brain microstructure.
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Affiliation(s)
- Hamza Kebiri
- CIBM Center for Biomedical Imaging, Switzerland; Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland; Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Ali Gholipour
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Rizhong Lin
- Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland; Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lana Vasung
- Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Camilo Calixto
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Željka Krsnik
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davood Karimi
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meritxell Bach Cuadra
- CIBM Center for Biomedical Imaging, Switzerland; Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
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Ciceri T, Casartelli L, Montano F, Conte S, Squarcina L, Bertoldo A, Agarwal N, Brambilla P, Peruzzo D. Fetal brain MRI atlases and datasets: A review. Neuroimage 2024; 292:120603. [PMID: 38588833 DOI: 10.1016/j.neuroimage.2024.120603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024] Open
Abstract
Fetal brain development is a complex process involving different stages of growth and organization which are crucial for the development of brain circuits and neural connections. Fetal atlases and labeled datasets are promising tools to investigate prenatal brain development. They support the identification of atypical brain patterns, providing insights into potential early signs of clinical conditions. In a nutshell, prenatal brain imaging and post-processing via modern tools are a cutting-edge field that will significantly contribute to the advancement of our understanding of fetal development. In this work, we first provide terminological clarification for specific terms (i.e., "brain template" and "brain atlas"), highlighting potentially misleading interpretations related to inconsistent use of terms in the literature. We discuss the major structures and neurodevelopmental milestones characterizing fetal brain ontogenesis. Our main contribution is the systematic review of 18 prenatal brain atlases and 3 datasets. We also tangentially focus on clinical, research, and ethical implications of prenatal neuroimaging.
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Affiliation(s)
- Tommaso Ciceri
- NeuroImaging Lab, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy; Department of Information Engineering, University of Padua, Padua, Italy
| | - Luca Casartelli
- Theoretical and Cognitive Neuroscience Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Florian Montano
- Diagnostic Imaging and Neuroradiology Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Stefania Conte
- Psychology Department, State University of New York at Binghamton, New York, USA
| | - Letizia Squarcina
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Alessandra Bertoldo
- Department of Information Engineering, University of Padua, Padua, Italy; Padova Neuroscience Center, University of Padua, Padua, Italy
| | - Nivedita Agarwal
- Diagnostic Imaging and Neuroradiology Unit, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
| | - Paolo Brambilla
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy; Department of Neurosciences and Mental Health, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Denis Peruzzo
- NeuroImaging Lab, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, Italy
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Garcia KE, Wang X, Santiago SE, Bakshi S, Barnes AP, Kroenke CD. Longitudinal MRI of the developing ferret brain reveals regional variations in timing and rate of growth. Cereb Cortex 2024; 34:bhae172. [PMID: 38679479 PMCID: PMC11056283 DOI: 10.1093/cercor/bhae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/22/2024] [Accepted: 04/04/2024] [Indexed: 05/01/2024] Open
Abstract
Normative ferret brain development was characterized using magnetic resonance imaging. Brain growth was longitudinally monitored in 10 ferrets (equal numbers of males and females) from postnatal day 8 (P8) through P38 in 6-d increments. Template T2-weighted images were constructed at each age, and these were manually segmented into 12 to 14 brain regions. A logistic growth model was used to fit data from whole brain volumes and 8 of the individual regions in both males and females. More protracted growth was found in males, which results in larger brains; however, sex differences were not apparent when results were corrected for body weight. Additionally, surface models of the developing cortical plate were registered to one another using the anatomically-constrained Multimodal Surface Matching algorithm. This, in turn, enabled local logistic growth parameters to be mapped across the cortical surface. A close similarity was observed between surface area expansion timing and previous reports of the transverse neurogenic gradient in ferrets. Regional variation in the extent of surface area expansion and the maximum expansion rate was also revealed. This characterization of normative brain growth over the period of cerebral cortex folding may serve as a reference for ferret studies of brain development.
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Affiliation(s)
- Kara E Garcia
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Evansville, IN 47715, United States
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Xiaojie Wang
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, United States
| | - Sarah E Santiago
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239, United States
| | - Stuti Bakshi
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, United States
| | - Anthony P Barnes
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR 97239, United States
| | - Christopher D Kroenke
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, United States
- Oregon Health and Science Advanced Imaging Research Center, Portland, OR 97239, United States
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Wagstyl K, Adler S, Seidlitz J, Vandekar S, Mallard TT, Dear R, DeCasien AR, Satterthwaite TD, Liu S, Vértes PE, Shinohara RT, Alexander-Bloch A, Geschwind DH, Raznahan A. Transcriptional cartography integrates multiscale biology of the human cortex. eLife 2024; 12:RP86933. [PMID: 38324465 PMCID: PMC10945526 DOI: 10.7554/elife.86933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
The cerebral cortex underlies many of our unique strengths and vulnerabilities, but efforts to understand human cortical organization are challenged by reliance on incompatible measurement methods at different spatial scales. Macroscale features such as cortical folding and functional activation are accessed through spatially dense neuroimaging maps, whereas microscale cellular and molecular features are typically measured with sparse postmortem sampling. Here, we integrate these distinct windows on brain organization by building upon existing postmortem data to impute, validate, and analyze a library of spatially dense neuroimaging-like maps of human cortical gene expression. These maps allow spatially unbiased discovery of cortical zones with extreme transcriptional profiles or unusually rapid transcriptional change which index distinct microstructure and predict neuroimaging measures of cortical folding and functional activation. Modules of spatially coexpressed genes define a family of canonical expression maps that integrate diverse spatial scales and temporal epochs of human brain organization - ranging from protein-protein interactions to large-scale systems for cognitive processing. These module maps also parse neuropsychiatric risk genes into subsets which tag distinct cyto-laminar features and differentially predict the location of altered cortical anatomy and gene expression in patients. Taken together, the methods, resources, and findings described here advance our understanding of human cortical organization and offer flexible bridges to connect scientific fields operating at different spatial scales of human brain research.
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Affiliation(s)
- Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College LondonLondonUnited Kingdom
| | - Sophie Adler
- UCL Great Ormond Street Institute for Child HealthHolbornUnited Kingdom
| | - Jakob Seidlitz
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt UniversityNashvilleUnited States
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Psychiatry, Harvard Medical SchoolBostonUnited States
| | - Richard Dear
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Alex R DeCasien
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Theodore D Satterthwaite
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of MedicinePhiladelphiaUnited States
| | - Siyuan Liu
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Petra E Vértes
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
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10
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Demirci N, Holland MA. Scaling patterns of cortical folding and thickness in early human brain development in comparison with primates. Cereb Cortex 2024; 34:bhad462. [PMID: 38271274 DOI: 10.1093/cercor/bhad462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 01/27/2024] Open
Abstract
Across mammalia, brain morphology follows specific scaling patterns. Bigger bodies have bigger brains, with surface area outpacing volume growth, resulting in increased foldedness. We have recently studied scaling rules of cortical thickness, both local and global, finding that the cortical thickness difference between thick gyri and thin sulci also increases with brain size and foldedness. Here, we investigate early brain development in humans, using subjects from the Developing Human Connectome Project, scanned shortly after pre-term or full-term birth, yielding magnetic resonance images of the brain from 29 to 43 postmenstrual weeks. While the global cortical thickness does not change significantly during this development period, its distribution does, with sulci thinning, while gyri thickening. By comparing our results with our recent work on humans and 11 non-human primate species, we also compare the trajectories of primate evolution with human development, noticing that the 2 trends are distinct for volume, surface area, cortical thickness, and gyrification index. Finally, we introduce the global shape index as a proxy for gyrification index; while correlating very strongly with gyrification index, it offers the advantage of being calculated only from local quantities without generating a convex hull or alpha surface.
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Affiliation(s)
- Nagehan Demirci
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Maria A Holland
- Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556, United States
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, United States
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Payette K, Li HB, de Dumast P, Licandro R, Ji H, Siddiquee MMR, Xu D, Myronenko A, Liu H, Pei Y, Wang L, Peng Y, Xie J, Zhang H, Dong G, Fu H, Wang G, Rieu Z, Kim D, Kim HG, Karimi D, Gholipour A, Torres HR, Oliveira B, Vilaça JL, Lin Y, Avisdris N, Ben-Zvi O, Bashat DB, Fidon L, Aertsen M, Vercauteren T, Sobotka D, Langs G, Alenyà M, Villanueva MI, Camara O, Fadida BS, Joskowicz L, Weibin L, Yi L, Xuesong L, Mazher M, Qayyum A, Puig D, Kebiri H, Zhang Z, Xu X, Wu D, Liao K, Wu Y, Chen J, Xu Y, Zhao L, Vasung L, Menze B, Cuadra MB, Jakab A. Fetal brain tissue annotation and segmentation challenge results. Med Image Anal 2023; 88:102833. [PMID: 37267773 DOI: 10.1016/j.media.2023.102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 03/16/2023] [Accepted: 04/20/2023] [Indexed: 06/04/2023]
Abstract
In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, gray matter, white matter, ventricles, cerebellum, brainstem, deep gray matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.
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Affiliation(s)
- Kelly Payette
- Center for MR Research, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland.
| | - Hongwei Bran Li
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Informatics, Technical University of Munich, Munich, Germany
| | - Priscille de Dumast
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; CIBM, Center for Biomedical Imaging, Lausanne, Switzerland
| | - Roxane Licandro
- Laboratory for Computational Neuroimaging, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA, United States; Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab (CIR), Medical University of Vienna, Vienna, Austria
| | - Hui Ji
- Center for MR Research, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | | | | | | | - Hao Liu
- Shanghai Jiaotong University, China
| | | | | | - Ying Peng
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Juanying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Huiquan Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Guiming Dong
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Fu
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Guotai Wang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - ZunHyan Rieu
- Research Institute, NEUROPHET Inc., Seoul 06247, South Korea
| | - Donghyeon Kim
- Research Institute, NEUROPHET Inc., Seoul 06247, South Korea
| | - Hyun Gi Kim
- Department of Radiology, The Catholic University of Korea, Eunpyeong St. Mary's Hospital, Seoul 06247, South Korea
| | - Davood Karimi
- Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Ali Gholipour
- Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Helena R Torres
- Algoritmi Center, School of Engineering, University of Minho, Guimarães, Portugal; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga Guimarães, Portugal
| | - Bruno Oliveira
- Algoritmi Center, School of Engineering, University of Minho, Guimarães, Portugal; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga Guimarães, Portugal
| | - João L Vilaça
- 2Ai - School of Technology, IPCA, Barcelos, Portugal
| | - Yang Lin
- Department of Computer Science, Hong Kong University of Science and Technology, China
| | - Netanell Avisdris
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel; Sagol Brain Institute, Tel Aviv Sourasky Medical Center, Israel
| | - Ori Ben-Zvi
- Sagol Brain Institute, Tel Aviv Sourasky Medical Center, Israel; Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Dafna Ben Bashat
- Sagol School of Neuroscience, Tel Aviv University, Israel; Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Lucas Fidon
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, United Kingdom
| | - Michael Aertsen
- Department of Radiology, University Hospitals Leuven, Leuven 3000, Belgium
| | - Tom Vercauteren
- School of Biomedical Engineering & Imaging Sciences, King's College London, London SE1 7EU, United Kingdom
| | - Daniel Sobotka
- Computational Imaging Research Lab, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Georg Langs
- Computational Imaging Research Lab, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Mireia Alenyà
- BCN-MedTech, Department of Information and Communications Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria Inmaculada Villanueva
- Department of Information and Communications Technologies, Universitat Pompeu Fabra, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Oscar Camara
- BCN-MedTech, Department of Information and Communications Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Bella Specktor Fadida
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Leo Joskowicz
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel
| | - Liao Weibin
- School of Computer Science, Beijing Institute of Technology, China
| | - Lv Yi
- School of Computer Science, Beijing Institute of Technology, China
| | - Li Xuesong
- School of Computer Science, Beijing Institute of Technology, China
| | - Moona Mazher
- Department of Computer Engineering and Mathematics, University Rovira i Virgili,Spain
| | | | - Domenec Puig
- Department of Computer Engineering and Mathematics, University Rovira i Virgili,Spain
| | - Hamza Kebiri
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; CIBM, Center for Biomedical Imaging, Lausanne, Switzerland
| | - Zelin Zhang
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Yuquan Campus, Hangzhou, China
| | - Xinyi Xu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Yuquan Campus, Hangzhou, China
| | - Dan Wu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Yuquan Campus, Hangzhou, China
| | | | - Yixuan Wu
- Zhejiang University, Hangzhou, China
| | | | - Yunzhi Xu
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Yuquan Campus, Hangzhou, China
| | - Li Zhao
- Key Laboratory for Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Yuquan Campus, Hangzhou, China
| | - Lana Vasung
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, United States; Department of Pediatrics, Harvard Medical School, United States
| | - Bjoern Menze
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Meritxell Bach Cuadra
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; CIBM, Center for Biomedical Imaging, Lausanne, Switzerland
| | - Andras Jakab
- Center for MR Research, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland; University Research Priority Project Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zürich, Zurich, Switzerland
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Kebiri H, Gholipour A, Vasung L, Krsnik Ž, Karimi D, Cuadra MB. Deep learning microstructure estimation of developing brains from diffusion MRI: a newborn and fetal study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.01.547351. [PMID: 37425859 PMCID: PMC10327173 DOI: 10.1101/2023.07.01.547351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. Fiber orientation distribution functions (FODs) are a common way of representing the orientation and density of white matter fibers. However, with standard FOD computation methods, accurate estimation of FODs requires a large number of measurements that usually cannot be acquired for newborns and fetuses. We propose to overcome this limitation by using a deep learning method to map as few as six diffusion-weighted measurements to the target FOD. To train the model, we use the FODs computed using multi-shell high angular resolution measurements as target. Extensive quantitative evaluations show that the new deep learning method, using significantly fewer measurements, achieves comparable or superior results to standard methods such as Constrained Spherical Deconvolution. We demonstrate the generalizability of the new deep learning method across scanners, acquisition protocols, and anatomy on two clinical datasets of newborns and fetuses. Additionally, we compute agreement metrics within the HARDI newborn dataset, and validate fetal FODs with post-mortem histological data. The results of this study show the advantage of deep learning in inferring the microstructure of the developing brain from in-vivo dMRI measurements that are often very limited due to subject motion and limited acquisition times, but also highlight the intrinsic limitations of dMRI in the analysis of the developing brain microstructure. These findings, therefore, advocate for the need for improved methods that are tailored to studying the early development of human brain.
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Affiliation(s)
- Hamza Kebiri
- CIBM Center for Biomedical Imaging, Switzerland
- Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ali Gholipour
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Lana Vasung
- Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, Massachusetts, USA
| | - Željka Krsnik
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davood Karimi
- Computational Radiology Laboratory, Department of Radiology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Meritxell Bach Cuadra
- CIBM Center for Biomedical Imaging, Switzerland
- Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
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