/BigBrain_BigBrainWarp_Support

BigBrain Warp Support

BigBrain

The BigBrain is the brain of a 65 year old man with no neurological or psychiatric diseases in clinical records at time of death. The brain was embedded in paraffin and sectioned in 7404 coronal histological sections (20 microns), stained for cell bodies. BigBrain is the digitized reconstruction of the hi-res histological sections (20 microns isotropic).

Dataset content

This dataset contains MSM spherical transformations to resample labels and fields between the BigBrain surface and 3 other major reference surfaces: FreeSurfer's fsaverage, Human Connectome Project's (HCP) fs_LR, and CIVET's MNI152. This dataset has been derived from the BigBrain release 2015 published in the BigBrain Project website.

Required files and some examples are provided here to illustrate how to use these transformations. Instructions are detailed to guide you through the conversion, mapping, and visualization steps. Using these examples, you should be able to resample any set of labels or field of your choosing (.annot, .label.gii, .shape.gii, .txt) between the BigBrain surface to/from the fsavg, fs_LR, and CIVET MNI152 surface templates. These transformations will also be included in the BigBrainWarp Project, a toolbox which aims to enable integration of BigBrain with neuroimaging and other neurobiological modalities.

You will need to install the following tools:

  • FreeSurfer

  • HCP workbench

  • MSM: You do not need to install MSM, but it was used to produce the transformation spheres provided in this release.

Note: The brain-view surface viewer is part of the MNI CIVET tools and is difficult to install. You may alternately use BrainBrowser for visualizing .obj and .txt.

Reference and more information

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 more information please visit the BigBrain Project website.