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   ## BigBrain June 2013 Data Release Frequently Asked Questions ##
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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 are all the volumes listed in the table?
A: The volumes are represented in either stereotaxic space (MNI-ICBM152 or
   MNI-SYN24) or in native histological space. The stereotaxic registration
   is not perfect but it is very good. The templates for registration 
   (ICBM152 and SYN24) 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 cannot be created because they are too large for the 
   data converter.

Q: How can I download the MINC volumes? The files appear incomplete.
A: Your browser may be limiting the maximum size of the file to transfer.
   This is problematic for the 100-micron MINC 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 at:
   http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage.
   The viewers are called register and Display.

Q: How do I view the volumes online?
A: The web-based viewer is TissueStack. Documentation is available at:
   http://www.tissuestack.org/.
   As you will soon discover, there is a limitation in the zoom factor in
   TissueStack.

Q: How can I view the OBJ surfaces?
A: The OBJ surfaces are viewable in Brainbrowser: 
   https://brainbrowser.cbrain.mcgill.ca, Surfstat (MATLAB-based) toolbox: 
   http://www.math.mcgill.ca/keith/surfstat, brain-view: 
   https://wiki.mouseimaging.ca/display/MICePub/brain-view, overlaid on the 
   corresponding volume in Display, etc.

Q: Is there an MRI of the bigbrain?
A: Yes, there is one of the fixed brain (removed from skull). It has an
   isotropic voxel size resolution of 0.444mm, and is available in the
   Raw_Data/MRI subdirectory. Note that the current version is in 
   "processing space" with y-z axes flipped. A new one in proper histological
   space will be supplied soon.

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.

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: https://filezilla-project.org), but not a web browser.
     % ftp bigbrain.loris.ca
   (enter anonymous as the username and your e-mail as the password)
   Use the command "ls" to list the contents, "cd" to change directory,
   "get" to download files.