Segmentation of the human cerebellar cortex from histological data has been considered a challenge due to its convoluted structure, and the numerous artifacts caused by sectioning or staining. The high resolution BigBrain model (Amunts et al., 2013) enables to overcome the lack of detail occasioned by the limited number of sections in existing datasets, and the large BigBrain data is ideal for...
Reference brain cortical surfaces derived from various structural pipelines enable integration of multimodal data into a standard space. In the absence of a common framework across structural pipelines, high profile surface atlases created within FreeSurfer (fsaverage) or Human Connectome Project (fs_LR) are not available in standard reference frames like the MNI152 or the 3D-reconstructed...
Magnetic resonance imaging (MRI) studies show that the majority of the T1-weighted contrast stems from myeloarchitecture, but cytoarchitecture still has an impact on the signal. Many cortical MRI markers are thought of as being driven mostly by myelin. Here, we compare the spatial organization and age effects of cortical thickness (CT) to 3 measures of cortical microstructure (gray-white...
We propose a 3D surface extraction benchmarking tool to evaluate the performance of 3D model extraction methods from 2D discrete label maps. We have used one geometrical and one anatomical model as references. The anatomical model is selected from the BigBrain hypothalamus atlas (Jones et al. in prep).
3D triangular meshes are used as ground truth 3D surfaces. These contain various...
The expansion of the cerebro-cerebellar system may be a primary driving factor behind primate cognitive evolution. Due to extensive connectivity to cognitive parts of the neocortex, the cerebellum is thought to support cognition analogous to its role in motor functions. Using an extensive MRI dataset (34 primates; 65 specimens) we found that cerebellar and...
The cerebral cortex consists of distinct layers with unique properties and functions. Previous work has shown that the laminar architecture of cortical regions varies in a spatially ordered fashion along a ‘‘sensory-fugal’’ axis, with decreasing laminar differentiation from the unimodal to transmodal areas. Indeed, the “Structural Model” proposes that the isocortex can be divided into regions...
Brain structure scaffolds intrinsic function, supporting cognition and ultimately behavioral flexibility. To evaluate the association between structure and function we assessed whether regions with similar microstructure would also be functionally connected in humans and macaques. This microstructural profile similarity approach has been previously developed in the big brain (Paquola, 2018)....
In current neuroimaging analyses the hippocampus is typically modelled as a subcortical volume, but it is actually made up of a folded archicortical mantle, or ‘ribbon’. Representing the hippocampus as such can be leveraged to enable qualitatively new analyses, such as registration, despite inter-individual differences in gyrification and folding structure, through topological alignment....
Analysis and visualization of big data, such as 3D reconstructions of human brain models from high resolution histological sections, requires a large amount of time and HPC resources to compute and to store the results of respective computations. And becomes prohibitively expensive to perform on the whole dataset during iterative development workflows, where multiple versions need to coexist...
In recent years, three-dimensional polarized light imaging (3D-PLI) has opened new avenues for measuring and analyzing nerve fiber orientations in postmortem brains at the micrometer scale. The raw data consists of 18 or 9-channel images, while common derived formats include transmittance, retardation, inclination and computed fiber orientation maps. These measurements are highly detailed and...
