1
|
Wang Q, Zhao S, Liu T, Han J, Liu C. Temporal fingerprints of cortical gyrification in marmosets and humans. Cereb Cortex 2023; 33:9802-9814. [PMID: 37434368 PMCID: PMC10656951 DOI: 10.1093/cercor/bhad245] [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: 02/18/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 07/13/2023] Open
Abstract
Recent neuroimaging studies in humans have reported distinct temporal dynamics of gyri and sulci, which may be associated with putative functions of cortical gyrification. However, the complex folding patterns of the human cortex make it difficult to explain temporal patterns of gyrification. In this study, we used the common marmoset as a simplified model to examine the temporal characteristics and compare them with the complex gyrification of humans. Using a brain-inspired deep neural network, we obtained reliable temporal-frequency fingerprints of gyri and sulci from the awake rs-fMRI data of marmosets and humans. Notably, the temporal fingerprints of one region successfully classified the gyrus/sulcus of another region in both marmosets and humans. Additionally, the temporal-frequency fingerprints were remarkably similar in both species. We then analyzed the resulting fingerprints in several domains and adopted the Wavelet Transform Coherence approach to characterize the gyro-sulcal coupling patterns. In both humans and marmosets, sulci exhibited higher frequency bands than gyri, and the two were temporally coupled within the same range of phase angles. This study supports the notion that gyri and sulci possess unique and evolutionarily conserved features that are consistent across functional areas, and advances our understanding of the functional role of cortical gyrification.
Collapse
Affiliation(s)
- Qiyu Wang
- School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shijie Zhao
- School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA 30602, United States
| | - Junwei Han
- School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Cirong Liu
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
2
|
Moghimi P, Dang AT, Do Q, Netoff TI, Lim KO, Atluri G. Evaluation of functional MRI-based human brain parcellation: a review. J Neurophysiol 2022; 128:197-217. [PMID: 35675446 DOI: 10.1152/jn.00411.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Brain parcellations play a crucial role in the analysis of brain imaging data sets, as they can significantly affect the outcome of the analysis. In recent years, several novel approaches for constructing MRI-based brain parcellations have been developed with promising results. In the absence of ground truth, several evaluation approaches have been used to evaluate currently available brain parcellations. In this article, we review and critique methods used for evaluating functional brain parcellations constructed using fMRI data sets. We also describe how some of these evaluation methods have been used to estimate the optimal parcellation granularity. We provide a critical discussion of the current approach to the problem of identifying the optimal brain parcellation that is suited for a given neuroimaging study. We argue that the criteria for an optimal brain parcellation must depend on the application the parcellation is intended for. We describe a teleological approach to the evaluation of brain parcellations, where brain parcellations are evaluated in different contexts and optimal brain parcellations for each context are identified separately. We conclude by discussing several directions for further research that would result in improved evaluation strategies.
Collapse
Affiliation(s)
- Pantea Moghimi
- Department of Neurobiology, University of Chicago, Chicago, Illinois
| | - Anh The Dang
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
| | - Quan Do
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
| | - Theoden I Netoff
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Kelvin O Lim
- Department of Psychiatry, University of Minnesota, Minneapolis, Minnesota
| | - Gowtham Atluri
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
| |
Collapse
|
3
|
Zhang S, Dong Q, Zhang W, Huang H, Zhu D, Liu T. Discovering hierarchical common brain networks via multimodal deep belief network. Med Image Anal 2019; 54:238-252. [PMID: 30954851 PMCID: PMC6487231 DOI: 10.1016/j.media.2019.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/04/2019] [Accepted: 03/27/2019] [Indexed: 01/08/2023]
Abstract
Studying a common architecture reflecting both brain's structural and functional organizations across individuals and populations in a hierarchical way has been of significant interest in the brain mapping field. Recently, deep learning models exhibited ability in extracting meaningful hierarchical structures from brain imaging data, e.g., fMRI and DTI. However, deep learning models have been rarely used to explore the relation between brain structure and function yet. In this paper, we proposed a novel multimodal deep believe network (DBN) model to discover and quantitatively represent the hierarchical organizations of common and consistent brain networks from both fMRI and DTI data. A prominent characteristic of DBN is that it is capable of extracting meaningful features from complex neuroimaging data with a hierarchical manner. With our proposed DBN model, three hierarchical layers with hundreds of common and consistent brain networks across individual brains are successfully constructed through learning a large dimension of representative features from fMRI/DTI data.
Collapse
Affiliation(s)
- Shu Zhang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Qinglin Dong
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Wei Zhang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA
| | - Heng Huang
- School of Automation, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Dajiang Zhu
- The University of Texas at Arlington, Arlington, TX 76010, USA
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, GA, USA.
| |
Collapse
|
4
|
Zhang S, Jiang X, Zhang W, Zhang T, Chen H, Zhao Y, Lv J, Guo L, Howell BR, Sanchez MM, Hu X, Liu T. Joint representation of connectome-scale structural and functional profiles for identification of consistent cortical landmarks in macaque brain. Brain Imaging Behav 2018; 13:1427-1443. [PMID: 30178424 DOI: 10.1007/s11682-018-9944-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Discovery and representation of common structural and functional cortical architectures has been a significant yet challenging problem for years. Due to the remarkable variability of structural and functional cortical architectures in human brain, it is challenging to jointly represent a common cortical architecture which can comprehensively encode both structure and function characteristics. In order to better understand this challenge and considering that macaque monkey brain has much less variability in structure and function compared with human brain, in this paper, we propose a novel computational framework to apply our DICCCOL (Dense Individualized and Common Connectivity-based Cortical Landmarks) and HAFNI (Holistic Atlases of Functional Networks and Interactions) frameworks on macaque brains, in order to jointly represent structural and functional connectome-scale profiles for identification of a set of consistent and common cortical landmarks across different macaque brains based on multimodal DTI and resting state fMRI (rsfMRI) data. Experimental results demonstrate that 100 consistent and common cortical landmarks are successfully identified via the proposed framework, each of which has reasonably accurate anatomical, structural fiber connection pattern, and functional correspondences across different macaque brains. This set of 100 landmarks offer novel insights into the structural and functional cortical architectures in macaque brains.
Collapse
Affiliation(s)
- Shu Zhang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Xi Jiang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Wei Zhang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Tuo Zhang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA.,School of Automation, Northwestern Polytechnical University, Xi'an, People's Republic of China
| | - Hanbo Chen
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Yu Zhao
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Jinglei Lv
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA.,School of Automation, Northwestern Polytechnical University, Xi'an, People's Republic of China
| | - Lei Guo
- School of Automation, Northwestern Polytechnical University, Xi'an, People's Republic of China
| | - Brittany R Howell
- Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA.,Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Institute of Child Development, University of Minnesota, Minneapolis, MN, USA
| | - Mar M Sanchez
- Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA. .,Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
| | - Xiaoping Hu
- Department of Bioengineering, UC Riverside, Riverside, CA, USA.
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA.
| |
Collapse
|
5
|
Canna A, Ponticorvo S, Russo AG, Manara R, Di Salle F, Saponiero R, Callaghan MF, Weiskopf N, Esposito F. A group-level comparison of volumetric and combined volumetric-surface normalization for whole brain analyses of myelin and iron maps. Magn Reson Imaging 2018; 54:225-240. [PMID: 30176374 DOI: 10.1016/j.mri.2018.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/17/2022]
Abstract
Quantitative MRI (qMRI) provides surrogate brain maps of myelin and iron content. After spatial normalization to a common standard brain space, these may be used to detect altered myelination and iron accumulation in clinical populations. Here, volumetric and combined volumetric and surface-based (CVS) normalization were compared to identify which procedure would afford the greatest sensitivity to inter-regional differences (contrast), and the lowest inter-subject variability (under normal conditions), of myelin- and iron-related qMRI parameters, in whole-brain group-level studies. Ten healthy volunteers were scanned twice at 3 Tesla. Three-dimensional T1-weighted, T2-weighted and multi-parametric mapping sequences for brain qMRI were used to map myelin and iron content over the whole brain. Parameter maps were spatially normalized using volumetric (DARTEL) and CVS procedures. Tissue probability weighting and isotropic Gaussian smoothing were integrated in DARTEL for voxel-based quantification (VBQ). Contrasts, coefficients of variations and sensitivity to detecting differences in the parameters were estimated in standard space for each approach on region of interest (ROI) and voxel-by-voxel bases. The contrast between cortical and subcortical ROIs with respectively different myelin and iron content was higher following CVS, compared to DARTEL-VBQ, normalization. Across cortical voxels, the inter-individual variability of myelin and iron qMRI maps were comparable between CVS (with no smoothing) and DARTEL-VBQ (with smoothing). CVS normalization of qMRI maps preserves higher myelin and iron contrast than DARTEL-VBQ over the entire brain, while exhibiting comparable variability in the cerebral cortex without extra smoothing. Thus, CVS may prove useful for detecting small microstructural differences in whole-brain group-level qMRI studies.
Collapse
Affiliation(s)
- Antonietta Canna
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Sara Ponticorvo
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Andrea G Russo
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Renzo Manara
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy
| | - Francesco Di Salle
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy; Department of Diagnostic Imaging, University Hospital "San Giovanni di Dio e Ruggi D'Aragona", Scuola Medica Salernitana, Salerno, Italy
| | - Renato Saponiero
- Department of Diagnostic Imaging, University Hospital "San Giovanni di Dio e Ruggi D'Aragona", Scuola Medica Salernitana, Salerno, Italy
| | - Martina F Callaghan
- Wellcome Centre for Human Neuroimaging, UCL Institute of Neurology, London, UK
| | - Nikolaus Weiskopf
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Fabrizio Esposito
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, University of Salerno, Baronissi, Salerno, Italy; Department of Diagnostic Imaging, University Hospital "San Giovanni di Dio e Ruggi D'Aragona", Scuola Medica Salernitana, Salerno, Italy.
| |
Collapse
|
6
|
Zhang T, Chen H, Razavi MJ, Li Y, Ge F, Guo L, Wang X, Liu T. Exploring 3-hinge gyral folding patterns among HCP Q3 868 human subjects. Hum Brain Mapp 2018; 39:4134-4149. [PMID: 29947164 DOI: 10.1002/hbm.24237] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/22/2018] [Accepted: 05/21/2018] [Indexed: 12/21/2022] Open
Abstract
Comparison and integration of neuroimaging data from different brains and populations are fundamental in neuroscience. Over the past decades, the neuroimaging field has largely depended on image registration to compare and integrate neuroimaging data from individuals in a common reference space, with a basic assumption that the brains are similar. However, the intrinsic neuroanatomical complexity and huge interindividual cortical folding variation remain underexplored. Here we focus on a specific cortical convolution pattern, termed 3-hinge gyral folding, which is the conjunction of gyri from multiple orientations and has unique and consistent anatomically, structurally, and functionally connective patterns across subjects. By developing a novel shape descriptor and a two-stage clustering pipeline, we devise an automatic method to identify 3-hinges in the Human Connectome Project Q3 868 human brains, and further parameterize the complexity of such a pattern and quantify its regularity and variation in terms of 3-hinge number, position, and morphology. Our results not only exhibit the huge interindividual variations, but also reveal regular relationship between gyral hinges and other factors, such as their locations and cortical morphologies. It is found that "line-shape" cortices have relatively more consistent 3-hinge shape pattern distributions, and certain types of 3-hinge patterns favor particular cortical morphologies. In addition, more 3-hinges are found on "line-shape" cortices while their numbers vary more across subjects than those on "non-line-shape" cortices. This study adds new insights into a better understanding of the regularity and variability of human brain anatomy, and their functional aspects.
Collapse
Affiliation(s)
- Tuo Zhang
- Brain Decoding Research Center and School of Automation, Northwestern Polytechnical University Xi'an, Shaanxi, China
| | - Hanbo Chen
- Cortical Architecture Imaging and Discovery Lab Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, Georgia
| | - Mir Jalil Razavi
- College of Engineering, The University of Georgia, Athens, Georgia
| | - Yujie Li
- Cortical Architecture Imaging and Discovery Lab Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, Georgia
| | - Fangfei Ge
- Cortical Architecture Imaging and Discovery Lab Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, Georgia
| | - Lei Guo
- Brain Decoding Research Center and School of Automation, Northwestern Polytechnical University Xi'an, Shaanxi, China
| | - Xianqiao Wang
- College of Engineering, The University of Georgia, Athens, Georgia
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab Department of Computer Science and Bioimaging Research Center, The University of Georgia, Athens, Georgia
| |
Collapse
|
7
|
Zhang S, Zhao Y, Jiang X, Shen D, Liu T. Joint representation of consistent structural and functional profiles for identification of common cortical landmarks. Brain Imaging Behav 2018; 12:728-742. [PMID: 28597338 PMCID: PMC5722718 DOI: 10.1007/s11682-017-9736-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In the brain mapping field, there have been significant interests in representation of structural/functional profiles to establish structural/functional landmark correspondences across individuals and populations. For example, from the structural perspective, our previous studies have identified hundreds of consistent DICCCOL (dense individualized and common connectivity-based cortical landmarks) landmarks across individuals and populations, each of which possess consistent DTI-derived fiber connection patterns. From the functional perspective, a large collection of well-characterized HAFNI (holistic atlases of functional networks and interactions) networks based on sparse representation of whole-brain fMRI signals have been identified in our prior studies. However, due to the remarkable variability of structural and functional architectures in the human brain, it is challenging for earlier studies to jointly represent the connectome-scale structural and functional profiles for establishing a common cortical architecture which can comprehensively encode both structural and functional characteristics across individuals. To address this challenge, we propose an effective computational framework to jointly represent the structural and functional profiles for identification of consistent and common cortical landmarks with both structural and functional correspondences across different brains based on DTI and fMRI data. Experimental results demonstrate that 55 structurally and functionally common cortical landmarks can be successfully identified.
Collapse
Affiliation(s)
- Shu Zhang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Yu Zhao
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Xi Jiang
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA
| | - Dinggang Shen
- Department of Radiology and BRIC, University of North Carolina, Chapel Hill, NC, USA.
- Department of Brain and Cognitive Engineering, Korea University, Seoul, 02841, Republic of Korea.
| | - Tianming Liu
- Cortical Architecture Imaging and Discovery Lab, Department of Computer Science and Bioimaging Research Center, The University of Georgia, Boyd GSRC 420, Athens, GA, 30602, USA.
| |
Collapse
|
8
|
Mikhael S, Hoogendoorn C, Valdes-Hernandez M, Pernet C. A critical analysis of neuroanatomical software protocols reveals clinically relevant differences in parcellation schemes. Neuroimage 2018; 170:348-364. [DOI: 10.1016/j.neuroimage.2017.02.082] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 02/16/2017] [Accepted: 02/27/2017] [Indexed: 12/11/2022] Open
|