Q: What is the bigbrain?
A: The bigbrain is the brain of a 65yo man with no neurological or psychiatric diseases in clinical records at time of death. The brain was embedded in parafin and sectionned in 7404 coronal histological sections (20 microns), stained for cell bodies. The bigbrain is the digitized reconstruction of the hi-res histological sections (20 microns isotropic).
Q: What volumes of BigBrain are available?
A: The volumes are represented in either stereotaxic space (MNI-ICBM152 or MNI-ADNI) or in native histological space. The stereotaxic registration is not perfect but it is very good. The templates for registration (ICBM152 and ADNI) are made available in those tables. The bigbrain volumes are offered at 100, 200, 300, 400 microns isotropic in both MINC (.mnc) and NIfTI (.nii) formats.
Q: Why is the aligned bigbrain showing such strong asymmetry?
A: The asymmetry results from aligning the histology sections to the MRI of the brain after it was extracted from the skull and set in formalin. We do not have a post-mortem MRI of the undistorted brain inside the head.
Q: The intensities are wrong in the NIfTI volumes. How can I view them correctly?
A: There was a problem with the initial data conversion to NIfTI format. The NIfTI volumes have been replaced on Sept 3, 2013. You will have to download the new volumes to view them in fslview, mricron or afni tools.
Q: Where are the 100um NIfTI volumes?
A: The 100um NIfTI volumes could not be created initially because of file size limitations of the data converter. They are now available.
Q: How can I download the MINC volumes? The files appear incomplete.
A: Volumes in MINC and NIfTI can be downloaded from the ftp site or from LORIS. Your browser may be limiting the maximum size of the file to transfer. This may be problematic for the 100-micron volumes.
Q: How can I view the MINC volumes?
A: MINC is an imaging format developed at the MNI. To obtain binaries (mostly Linux and OSX) of the MINC tools, download the MINC Tool Kit. The viewers are called register and Display.
Q: How do I view the volumes online?
A: You can explore the high resolution human brain model online in the ebrains siibra explorer.
Q: How can I view the surfaces?
A: The MNI-OBJ surfaces are viewable in a web-based fashion using Brainbrowser or BigBrainbrowser. The surfaces are also available in various other formats (STL, gii, WaveFront-OBJ, etc) for viewing with other standard tools in the field.
Q: Is there a problem with surfaces in STL format?
A: The cortical surfaces in STL format are not overlaid properly onto the BigBrain volume when using 3DSlicer or Freeview. This is not a conversion issue but rather a problem with the viewing software requiring a transformation from world to voxel coordinates, which is not available within the STL format. As an alternative, you can view the surface in .gii format using these tools. Surfaces in STL are more useful for 3D printing.
Q: Is there an MRI of the bigbrain?
A: Yes, there is an MRI of the fixed brain (removed from skull) at an isotropic voxel size resolution of 0.444mm. Note that this MRI is in "processing space" with y-z axes flipped.
Q: How can I view the volumes as in the bigbrain videos?
A: The bigbrain videos were created using Atelier3D, a licensed software which is currently not distributed. The volume read in Atelier3D is at 20-micron isotropic, which is too big for file transfers. This is why reduced volumes at 100, 200, 300, 400 microns have been created. You can explore the BigBrain online in the ebrains siibra explorer.
Q: Is there sound to the bigbrain videos?
A: No.
Q: Is there a way to mass-download the data files?
A: Yes. As of March 12th, 2014, all sections and volumes are available on an anonymous FTP server located at the same address as this site. We recommend connecting to the FTP server using a command line or GUI client (e.g., Filezilla, but not a web browser).