Mapping the human cortical surface by combining quantitative T(1) with retinotopy.
TL;DR: R1 maps were reproducible within individuals and comparable between subjects without intensity normalization, enabling multi-center studies of development, aging, and disease progression, and structure/function mapping in other modalities.
Abstract: We combined quantitative relaxation rate (R1= 1/T1) mapping—to measure local myelination—with fMRI-based retinotopy. Gray–white and pial surfaces were reconstructed and used to sample R1 at different cortical depths. Like myelination, R1 decreased from deeper to superficial layers. R1 decreased passing from V1 and MT, to immediately surrounding areas, then to the angular gyrus. High R1 was correlated across the cortex with convex local curvature so the data was first “de-curved”. By overlaying R1 and retinotopic maps, we found that many visual area borders were associated with significant R1 increases including V1, V3A, MT, V6, V6A, V8/VO1, FST, and VIP. Surprisingly, retinotopic MT occupied only the posterior portion of an oval-shaped lateral occipital R1 maximum. R1 maps were reproducible within individuals and comparable between subjects without intensity normalization, enabling multi-center studies of development, aging, and disease progression, and structure/function mapping in other modalities.
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TL;DR: The minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space are described.
3,992 citations
TL;DR: An integrated approach to data acquisition, analysis and sharing that builds upon recent advances, particularly from the Human Connectome Project (HCP), and should accelerate progress in understanding the brain in health and disease.
Abstract: Noninvasive human neuroimaging has yielded many discoveries about the brain. Numerous methodological advances have also occurred, though inertia has slowed their adoption. This paper presents an integrated approach to data acquisition, analysis and sharing that builds upon recent advances, particularly from the Human Connectome Project (HCP). The 'HCP-style' paradigm has seven core tenets: (i) collect multimodal imaging data from many subjects; (ii) acquire data at high spatial and temporal resolution; (iii) preprocess data to minimize distortions, blurring and temporal artifacts; (iv) represent data using the natural geometry of cortical and subcortical structures; (v) accurately align corresponding brain areas across subjects and studies; (vi) analyze data using neurobiologically accurate brain parcellations; and (vii) share published data via user-friendly databases. We illustrate the HCP-style paradigm using existing HCP data sets and provide guidance for future research. Widespread adoption of this paradigm should accelerate progress in understanding the brain in health and disease.
793 citations
TL;DR: The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.
Abstract: Multi-center studies using magnetic resonance imaging facilitate studying small effect sizes, global population variance and rare diseases. The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points. The level of inter-site comparability is still controversial for conventional anatomical T1-weighted MRI data. Quantitative multi-parameter mapping (MPM) was designed to provide MR parameter measures that are comparable across sites and time points, i.e., 1mm high-resolution maps of the longitudinal relaxation rate (R1=1/T1), effective proton density (PD*), magnetization transfer saturation (MT) and effective transverse relaxation rate (R2*=1/T2*). MPM was validated at 3T for use in multi-center studies by scanning five volunteers at three different sites. We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV) for typical morphometric measures (i.e., gray matter probability maps used in voxel-based morphometry) and the four quantitative parameters. The inter-site bias and CoV were smaller than 3.1% and 8%, respectively, except for the inter-site CoV of R2* (< 20%). The gray matter probability maps based on the MT parameter maps had a 14% higher inter-site reproducibility than maps based on conventional T1-weighted images. The low inter-site bias and variance in the parameters and derived gray matter probability maps confirm the high comparability of the quantitative maps across sites and time points. The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.
452 citations
Cites background or methods from "Mapping the human cortical surface ..."
...An advanced MPM approach using a higher isotropic resolution of 800 μm even allowed for mapping of cortical myelination and parcellation of brain areas (Dick et al., 2012; Sereno et al., 2012)....
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...The multiple parameter maps and the high resolution allow for a detailed assessment of the white matter (WM) and gray matter (GM) tissue microstructure (Draganski et al., 2011; Dick et al., 2012; Sereno et al., 2012)....
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TL;DR: In this paper, a noninvasive neuroimaging measure, T1w/T2w mapping, was used to identify a hierarchical axis linking cortical transcription and anatomy, along which gradients of micro-scale properties may contribute to the macroscale specialization of cortical function.
Abstract: Hierarchy provides a unifying principle for the macroscale organization of anatomical and functional properties across primate cortex, yet microscale bases of specialization across human cortex are poorly understood. Anatomical hierarchy is conventionally informed by invasive tract-tracing measurements, creating a need for a principled proxy measure in humans. Moreover, cortex exhibits marked interareal variation in gene expression, yet organizing principles of cortical transcription remain unclear. We hypothesized that specialization of cortical microcircuitry involves hierarchical gradients of gene expression. We found that a noninvasive neuroimaging measure—MRI-derived T1-weighted/T2-weighted (T1w/T2w) mapping—reliably indexes anatomical hierarchy, and it captures the dominant pattern of transcriptional variation across human cortex. We found hierarchical gradients in expression profiles of genes related to microcircuit function, consistent with monkey microanatomy, and implicated in neuropsychiatric disorders. Our findings identify a hierarchical axis linking cortical transcription and anatomy, along which gradients of microscale properties may contribute to the macroscale specialization of cortical function.
414 citations
TL;DR: Using existing PET data and functional network parcellations, metabolic differences in the differently myelinated cortical functional networks are examined and found to be consistent with the hypothesis that intracortical myelination may stabilize intracordical circuits and inhibit synaptic plasticity.
370 citations
References
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TL;DR: A set of automated procedures for obtaining accurate reconstructions of the cortical surface are described, which have been applied to data from more than 100 subjects, requiring little or no manual intervention.
9,599 citations
"Mapping the human cortical surface ..." refers methods in this paper
...Widely applied post hoc histogram-based normalization methods (e.g. Dale et al. 1999) and T1w/T2 weighted (T2w) ratio methods (Glasser and Van Essen 2011) remain sensitive to the effects of uncorrected B1 “transmit” inhomogeneities (flip-angle variation) on brightness and contrast, which affect…...
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TL;DR: An automated method for accurately measuring the thickness of the cerebral cortex across the entire brain and for generating cross-subject statistics in a coordinate system based on cortical anatomy is presented.
Abstract: Accurate and automated methods for measuring the thickness of human cerebral cortex could provide powerful tools for diagnosing and studying a variety of neurodegenerative and psychiatric disorders. Manual methods for estimating cortical thickness from neuroimaging data are labor intensive, requiring several days of effort by a trained anatomist. Furthermore, the highly folded nature of the cortex is problematic for manual techniques, frequently resulting in measurement errors in regions in which the cortical surface is not perpendicular to any of the cardinal axes. As a consequence, it has been impractical to obtain accurate thickness estimates for the entire cortex in individual subjects, or group statistics for patient or control populations. Here, we present an automated method for accurately measuring the thickness of the cerebral cortex across the entire brain and for generating cross-subject statistics in a coordinate system based on cortical anatomy. The intersubject standard deviation of the thickness measures is shown to be less than 0.5 mm, implying the ability to detect focal atrophy in small populations or even individual subjects. The reliability and accuracy of this new method are assessed by within-subject test-retest studies, as well as by comparison of cross-subject regional thickness measures with published values.
5,171 citations
TL;DR: This work has developed a means for generating an average folding pattern across a large number of individual subjects as a function on the unit sphere and of nonrigidly aligning each individual with the average, establishing a spherical surface‐based coordinate system that is adapted to the folding pattern of each individual subject, allowing for much higher localization accuracy of structural and functional features of the human brain.
Abstract: The neurons of the human cerebral cortex are arranged in a highly folded sheet, with the majority of the cortical surface area buried in folds. Cortical maps are typically arranged with a topography oriented parallel to the cortical surface. Despite this unambiguous sheetlike geometry, the most commonly used coordinate systems for localizing cortical features are based on 3-D stereotaxic coordinates rather than on position relative to the 2-D cortical sheet. In order to address the need for a more natural surface-based coordinate system for the cortex, we have developed a means for generating an average folding pattern across a large number of individual subjects as a function on the unit sphere and of nonrigidly aligning each individual with the average. This establishes a spherical surface-based coordinate system that is adapted to the folding pattern of each individual subject, allowing for much higher localization accuracy of structural and functional features of the human brain.
3,024 citations
"Mapping the human cortical surface ..." refers background in this paper
...the cortical-surface-based cross-subject average (Fischl et al. 1999) of R1 from 6 subjects (2 R1 scans each), displayed on 1 of the 6 subjects’ surfaces....
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...Local curvature predicted R1 better than a measure of whether a cortical region was on a sulcus or gyrus (the primary measure used for cross-subject surface alignment; Fischl et al. 1999)....
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...The top 3 rows of Figure 2 show medial and lateral views of the cortical-surface-based cross-subject average (Fischl et al. 1999) of R1 from 6 subjects (2 R1 scans each), displayed on 1 of the 6 subjects’ surfaces....
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TL;DR: Cortical magnification factor curves for striate and extrastriate cortical areas were determined, which showed that human visual areas have a greater emphasis on the center-of-gaze than their counterparts in monkeys.
Abstract: The borders of human visual areas V1, V2, VP, V3, and V4 were precisely and noninvasively determined. Functional magnetic resonance images were recorded during phase-encoded retinal stimulation. This volume data set was then sampled with a cortical surface reconstruction, making it possible to calculate the local visual field sign (mirror image versus non-mirror image representation). This method automatically and objectively outlines area borders because adjacent areas often have the opposite field sign. Cortical magnification factor curves for striate and extrastriate cortical areas were determined, which showed that human visual areas have a greater emphasis on the center-of-gaze than their counterparts in monkeys. Retinotopically organized visual areas in humans extend anteriorly to overlap several areas previously shown to be activated by written words.
2,590 citations
"Mapping the human cortical surface ..." refers background or methods in this paper
...Cortical-surface-based functional magnetic resonance imaging retinotopy (Engel et al. 1994; Sereno et al. 1995; DeYoe et al. 1996) is now established and often combined with functional studies, which constitute the overwhelming majority of in vivo human neuroimaging experiments....
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...We then performed cortical-surface-based cross-subject averages of complexvalued (amplitude and phase) data (Sereno and Huang 2006; Hagler et al. 2007) and calculated visual field sign from the polar angle and eccentricity averages to identify borders in early areas (Sereno et al. 1995)....
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...2007) and calculated visual field sign from the polar angle and eccentricity averages to identify borders in early areas (Sereno et al. 1995)....
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...onance imaging retinotopy (Engel et al. 1994; Sereno et al. 1995; DeYoe et al. 1996) is now established and often combined with...
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TL;DR: A precisely defined method for automatically labeling the cortical surface in standard terminology using standard internationally accepted nomenclature and criteria is presented.
2,190 citations