Welcome to the BigBrain! This is the FTP site for the data releases of the BigBrain project. The BigBrain dataset is the result of a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich) and Dr. Alan Evans (Montreal Neurological Institute). Amunts, K. et al.: "BigBrain: An Ultrahigh-Resolution 3D Human Brain Model", Science (2013) 340 no. 6139 1472-1475, June 2013 https://www.sciencemag.org/content/340/6139/1472.abstract For research purposes only, no commercial use without written consent. The WWW site for the data release is here: https://bigbrain.loris.ca/ Technical support by email: cbrain-support.mni@mcgill.ca Content of subdirectories: * 'faq.txt' : Frequently Asked Questions (FAQ). * 'credits.txt' : Credits and acknowledgments. * 'References/' : BigBrain publications. * 'Raw_Data/' : Post-mortem MRI aligned to the block faces and raw sections in tiff format (1TB). This MRI is not in the aligned histological space. Use the MRI in the Release itself. A few raw sections at 1-micron are available, unaligned (these have been rescanned, so not aligned to the other raw images at 10-micron in mnc/ and Tiff/). * 'Media/' : Videos and pictures of the BigBrain based on the latest release. * 'Welcome.txt' : This file. * 'BigBrainRelease.XXXX : Official release in year XXXX. The Releases are based on the status of the non-linear section-to-section alignment. All files within a release are based on the same alignment and "fit" together. Do not mix files from different releases. They do not match. The 2013 release is based on the August 2012 alignment and was used for the publication of our Science paper, June 2013, and the HBM 2014 poster. The alignment was not fully converged and displayed many "jaggies" in the cross planes. The optical-balancing was based on a basic histogram-smoothing algorithm and variations in section intensities were still clearly visible in the model. Despite the short-comings, it was a great success. The 2015 release is based on the January 2015 alignment with global b-spline optical-balancing as the major achievement. The alignment is much smoother than in the 2013 release, albeit not perfect given the strong distortions in the raw images. The model looks really great now. The tissue classified volumes have been supplied. We are currently working the extraction of the cortical surfaces and registration to MNI ICBM152 space and MNI ADNI space (coming soon). Segmentation of deep brain structures is under way for this model. Contributions will be added to the Release as they become available. The contents of a Release are: * 3D_Volumes/ : The 3D histological volumes (Merker stain), at different isotropic resolutions (100, 200, 300, 400 microns), in MNI space and histological space, with and without optical- balancing, in MINC and NIfTI formats. The 100um volumes are too large to convert to NIfTI using the current version of our converter. The MNI ICBM152 2009b symmetric model used for the stereotaxic registration of the BigBrain can be found at http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009. The raw (non-optically-balanced) volumes are no longer supported in the 2015 release, white stereotaxic registration to the MNI ADNI is now supported. * 3D_Classified_Volumes/ : The 3D classified volumes for basic tissue classes (0=background, 1=CSF, 2=cortical gray, 3=white, 4=cerebellum, 5=Layer1 of cortex, 6=sub-cortical gray, 7=pineal gland, 8=cerebellum/brainstem gray, 9=cerebellum/brainstem white). The volumes are at the same isotropic resolutions as the 3D histological volumes. * 3D_Surfaces/ : The cortical surfaces for white and gray matter. The surfaces are stored in the .obj MNI format (some documentation at http://www.bic.mni.mcgill.ca/Services/HowToWorkWithObjectFiles), in NIfTI .gii format, and in STL .stl format for 3D printing. * 2D_Final_Sections/ : These are the final aligned sections in the coronal dimension as well as the reconstituted sections in the sagittal and axial dimensions. For each set, you will find the sections in the minc format and as lo-res and hi-res png images. * 3D_Blocks/ : These are blocks of the BigBrain at 40um. There are 5x5x5 blocks for a total of 125 blocks representing the BigBrain. There is a small overlap at block boundaries. * 3D_ROIs/ : These are blocks of specific regions of the BigBrain, like BA10, Central Sulcus, Hippocampus, etc, at various resolutions. * 3D_MRI/ : 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. * Layer_Segmentation/ : All layer segmentation files related to Konrad Wagstyl's paper (https://www.biorxiv.org/content/10.1101/580597v1) * A3D/ : These are the Atelier3d client files for viewing the BigBrain model. (Release 2015 only.) Legend of file identifiers: - .mnc : minc volume format (minc2) - .obj : MNI surface format - .nii : NIfTI volume format - .gii : NIfTI surface format - .stl : STL surface format - .png : png image format - 100um, 200um, 300um, 400um : isotropic voxel size in microns - neg : inverted image (black vs white background) - optbal : volume with optical-balancing - cls : tissue classification - 2009b_sym, regSyn24, ADNI : stereotaxic registration space - 8, 16 : bit encoding - left, right : hemisphere for surface - gray, white : type of cortical surface - 327680 : number of triangles in surface Future contributions, such as Atlases and A3D models, will be added to the new Releases. Please share your BigBrain success stories with us!