Welcome to the BigBrain Release 2015! This page lists the updates for Release 2015, namely newly added files based on the alignment of this release. Jan 19, 2024: * added masks for the various BigBrain surfaces. The masks for BigBrainWarp and CerebralCortex2018 are the same (based on Apr7_2016). The masks for April2019 and PLos2020 are the same, but different than those for Apr_2016 (need to ask K. Wagstyl). - BigBrainWarp_Support/white_surfaces/ - Layer_Segmentation/3D_Surfaces/CerebralCortex2018/ - Layer_Segmentation/3D_Surfaces/April2019/ - Layer_Segmentation/3D_Surfaces/PLoSBiology2020/ There were already masks in: - 3D_Surfaces/Apr7_2016/ Oct 14, 2023: * added masks for the hemispheres in 3D_Classified_Volumes (in histological space only) Sept 6, 2021: * .json files for MicroDraw in new MicroDraw directory. June 8, 2021: * Layer_Segmentation/3D_Surface/PLoSBiology2020/* : added the surfaces that were published by K. Wagstyl in PLoS Biology, 2020. These surfaces are in CIVET format, at 327680 triangles per hemisphere. Vertices match across layers. Layer0 is the pial surface. Layer6 is slightly deeper than the white surface defined by CIVET. Feb 24, 2021: * BigBrainWarp_Support/* : Transformation files to use with BigBrainWarp https://bigbrainwarp.readthedocs.io/en/latest/ Jan 22, 2021: * Restructuration of directories to split into mnc and nii subdirectories for volumes * Create all nii counterparts for mnc volumes * Create all gii, stl, wavefront-obj counterparts for MNI-obj surfaces Jan 15, 2021: * 3D_ROIs and 3D_Blocks now in both mnc and nii Apr 3, 2020: * Surface_Parcellations/* : BigBrain surfaces registered to standard surfaces (fs_LR, fsaverage, MNI-152), onto which surface parcellations can be projected (Brainnetome, DKT, Economo, Schaefer2018, HCP) * Surface_Parcellations/BigBrain_space/* : contains resampled atlases mapped to the original BigBrain surfaces * Surface_Parcellations/fsaverage/* : contains atlases defined on fsaverage with surface-based registration of BigBrain surfaces to fsaverage * Surface_Parcellations/fs_LR/* : contains atlases defined on fs_LR with surface-based registration of BigBrain surfaces to fs_LR * Surface_Parcellations/ReadMe.txt : documentation and references to cite if using this work Apr 3, 2020: * Hippocampus_Segmentation/* : surfaces for CA1, CA2, CA3, CA4, dendate gyrus, subiculum and mid-surface Apr 4, 2019: * Layer_Segmentation/* : Layer segmentation data for Konrad Wagstyl's paper: (https://www.biorxiv.org/content/10.1101/580597v1) * Layer_Segmentation/2D_Sections : the 6 cortical layers in BigBrain histological voxel space; contains minc and png for coronal sections only at this time. Note that the png images are qualitative to represent labels using a gray scale colour map. For the true label values, use the minc files. * Layer_Segmentation/3D_Surfaces : surfaces of the 6 cortical layers, left and right, 655362 vertices/ 1310720 triangles per side, in BigBrain histological space * Layer_Segmentation/Histological_Profiles : n/a * Layer_Segmentation/Manual_Annotations : the 6 cortical layers manually annotated on selected 2D coronal sections of BigBrain; used as training data for the automated segmentation Mar 15, 2018: * Layer_Segmentaion/3D_Surfaces/CerebralCortex : added the surfaces that were published by K. Wagstyl in Cerebral Cortex, 2018. Feb 27, 2018: * 3D_Classified_Volumes/Histological_Space : added tissue/CSF mask * 3D_Classified_Volumes/Histological_Space : added some final classified images at 200um full_cls_200um_mask.mnc = a brain mask, separating CSF from BG full_cls_200um_9classes.mnc = same as full_cls_200um.mnc, but cleaned up GM/WM for surface extraction full_cls_200um_mrisim.mnc = classified image suited for mrisim with BG, CSF, GM, SC, WM * MRISIM : created MRISIM folder for MRI simulated images of BigBrain (t1w, t2w). Nov 9, 2017: * 2D_Final_Sections/Coronal/SVG : * 2D_Final_Sections/Axial/SVG : * 2D_Final_Sections/Sagittal/SVG : added SVG files for cross-sections of cortical surfaces onto sections Aug 8, 2017: * 3D_Surfaces/Apr7_2016/MNI-obj : added surface mask of the medial wall and brainstem, both hemispheres. Aug 3, 2017: * 3D_MRI : added the MRI of BigBrain in the final histological space. Use this MRI to compare to the volumes in 3D_Volumes (histological space) of this release. Note that it does not fit perfectly. Do not use the MRI from the Raw_Data to compare to the aligned volumes. July 3, 2017: * 3D_Surfaces/Apr7_2016 : added surfaces in MNI ICBM152-2009b space (mnc) May 26, 2017: * 3D_ROIs : added block for cerebellum, in histological space Apr 21, 2017: * 3D_Surfaces : conversion to .stl format for 3-D printing. wow! Mar 30, 2017: * 3D_ROIs : added block for ventro-lateral pre-frontal cortex, right side, in histological space Jan 19, 2017: * A3D : Atelier3d client files for viewing the BigBrain model. Look inside this folder for specific documentation. Aug 22, 2016: * 3D_* : many more volumes converted to nii. July 18, 2016: * 3D_Classified_Volumes : classified volumes transformed to MNI ICBM152-2009b space (mnc and nii). July 11, 2016: * 3D_Surfaces/Apr7_2016 : conversion to .gii format. June 20, 2016: * 3D_ROIs/Hypothalamus : new blocks for the hypothalamus (left+right combined) with extended coverage, at various voxel resolutions, in histological space. Old blocks are gone. June 8, 2016: * 3D_ROIs/Hypothalamus : blocks for the hypothalamus (left+right combined), at various voxel resolutions, in histological space. June 1, 2016: * 3D_ROIs/Hippocampus : blocks providing full coverage of the hippocampus, at various voxel resolutions, in histological space. May 18, 2016: * 3D_Volumes/MNI-ADNI_Space : * 3D_Volumes/MNI-ICBM152_Space : The minc volumes have finally been resampled and copied here. Still to come: the version in .nii. Feb 24, 2016: * 2D_Final_Sections/Coronal/Dzi : 2D_Final_Sections/Sagittal/Dzi : 2D_Final_Sections/Axial/Dzi : These are the full resolution (20um) png images in DZI format (ImageMagick DeepZoom) and can be viewed with OpenSeadragon (web-based). * 3D_Classified_Volumes : * 3D_Volumes/Histological_Space : Full volumes in histological space have been moved here. * 3D_Volumes/MNI-ADNI_Space : Full volumes resampled in the MNI-ADNI. There are also the linear and non-linear transformations from histological space to ICBM152 space. You have to apply the linear transform first before applying the non-linear transform. * 3D_Volumes/MNI-ICBM152_Space : Full volumes resampled in the MNI-ICBM152. There are also the linear and non-linear transformations from histological space to ICBM152 space. You have to apply the linear transform first before applying the non-linear transform. * 3D_Blocks : These are blocks at high-resolution (40um) in histological space that together compose the entire BigBrain (with white background and a few mm overlap). The legend volume indicates in which block a voxel at (x,y,z) lies in. Contact us if you want blocks at other resolutions. * 3D_ROIs : These are regional blocks at various resolutions of common regions of interest like visual cortex, hippocampus, etc., in histological space. Contact us if you want a special block that is not available in this list. * 3D_Surfaces : Gray/white surfaces (raw and resampled) in MNI .obj format, in histological space and in MNI ICBM152-200b space. These surfaces are stored by dates of creation since they are routinely extracted after corrections to the classified image at 200um. Also available in .gii (NIFTI) and .stl (STL format for 3D printing).