CONP Portal | Dataset
BigBrain dataset - BigBrainWarp Support (derived dataset)
| Is About: | Homo sapiens, adult |
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Description:
Dataset README information
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:
-
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.
The following instructions require a basic understanding of UNIX/LINUX command lines. A subset of open datasets on the Portal are also available through a browser-based download button. The instructions below regard dataset download with the use of DataLad. To install DataLad on your system, please refer to the install section of the DataLad Handbook .
Note: For maximum compatibility with conp-dataset, the CONP recommends versions 3.12+ of Python, 10.20241202+ of git-annex, and 1.1.4+ of datalad.
1) Initiate the CONP dataset
Run the following command in the directory where you want the CONP dataset (conp-dataset) to be installed:
2) Install the BigBrain_BigBrainWarp_Support dataset
To install the BigBrain_BigBrainWarp_Support dataset, run the following commands to move into the "projects" subdirectory under the "conp-dataset" directory (created in the previous step) and run datalad install:
3) Download data from the BigBrain_BigBrainWarp_Support dataset
Now that the dataset has been installed, go into the BigBrain_BigBrainWarp_Support dataset directory.
The files visible after installing the dataset but before downloading (in the next step) are symbolic links and need to be downloaded manually using the datalad get command:
If you run datalad get * command, all the files available in the dataset directory will be downloaded.
Experiments - Beta