BigBrainMRICoreg

This dataset includes co-registration of the BigBrain dataset to the MNI PD25 atlas and the ICBM152 2009b atlases.
The data include deformed BigBrain atlases and manual subcortical segmentations in MINC2 and NIFTI-1 formats, as well as relevant spatial transformation in MINC transformation format.
The segmented subcortical structures include: red nucleus, subthalamic nucleus, substantia nigra, caudate, putamen, globus pallidus externa, globus pallidus interna, thalamus, hippocampus, nucleus
accumbens, and amygdala

Note that the described improved co-registration was performed upon the BigBrain data in ICBM space from the BigBrain 2015release.

Within this dataset, the down-sampled versions of BigBrain atlases are distributed under the CC BY4.0 License upon the consent from the original data owners, the Montreal Neurological Institute
(Montreal, Canada) and the Forschungszentrum Jülich (Jülich, Germany). However, this exception to the existing BigBrain dataset does not alter the general term of that license for use of the
BigBrain itself, which is still under the CC BY-NC-SA 4.0 License.

The included files are as follows:

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1. Deformed BigBrain atlases & MRI templates:
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BigBrain in PD25 space: sub-BigBrain_rez-{300um, 500um, 1mm}_space-PD25_histology.nii.gz
BigBrain in ICBM152 symmetric atlas: sub-BigBrain_rez-{300um, 500um, 1mm}_space-ICBM2009sym_histology.nii.gz
BigBrain in ICBM152 asymmetric atlas: sub-BigBrain_rez-{300um, 500um, 1mm}_space-ICBM2009asym_histology.nii.gz

Synthetic T2w PD25 atlas: sub-PD25_rez-{300um,500um,1mm}_SynT2w.nii.gz
T1-T2* fusion PD25 atlas: sub-PD25_rez-{300um,500um,1mm}_T1T2starfusion.nii.gz
T1w PD25 atlas: sub-PD25_rez-{300um,500um,1mm}_T1w.nii.gz
PD25 atlas brain mask: sub-PD25_rez-500um_brainmask.nii.gz
T1w ICBM152 2009b symmetric atlas: sub-ICBM2009asym_rez-500um_T1w.nii.gz
T2w ICBM152 2009b symmetric atlas: sub-ICBM2009asym_rez-500um_T2w.nii.gz
T1w ICBM152 2009b asymmetric atlas: sub-ICBM2009asym_rez-500um_T1w.nii.gz
T2w ICBM152 2009b asymmetric atlas: sub-ICBM2009asym_rez-500um_T2w.nii.gz

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2. Manual subcortical segmentations:
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BigBrain coregistered to ICBM in the *BigBrain2015* release: sub-BigBrain_rez-{300um,500um}_space-ICBMoriginal_atlas.nii.gz
MNI PD25: sub-PD25_rez-500um_atlas.nii.gz
ICBM152 2009b symmetric: sub-ICBM2009asym_rez-500um_atlas.nii.gz
ICMB152 2009b asymmetric: sub-ICBM2009asym_rez-500um_atlas.nii.gz

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3. Related transformations:
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As the spatial transformations that deform BigBrain to PD25 and ICBM atlases were in MINC format, please download them via
https://osf.io/xkqb3/
http://nist.mni.mcgill.ca/?p=1209

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4. Manual segmentation labels:
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Label,Nuclei
1,left red nucleus
2,right red nucleus
3,left substantia nigra
4,right substantia nigra
5,left subthalamic nucleus
6,right subthalamic nucleus
7,left caudate
8,right caudate
9,left putamen
10,right putamen
11,left globus pallidus externa
12,right globus pallidus externa
13,left globus pallidus interna
14,right globus pallidus Interna
15,left thalamus
16,right thalamus
17,left hippocampus
18,right hippocampus
19,left nucleus accumbens
20,right nucleus accumbens
21,left amygdala
22,right amygdala

References:

For the methods used, please cite the following articles:
1. Y. Xiao, J.C. Lau, T. Anderson,J. DeKraker, D. Louis Collins, T.M. Peters, and A.R. Khan, “An accurate registration of the BigBrain dataset with the MNI PD25 and ICBM152 atlases,” Scientific Data, 6(1),1-9, 2019.

2.Y. Xiao, V. Fonov, S. Beriault, F.A. Subaie, M.M. Chakravarty, A.F. Sadikot, G. Bruce Pike, and D. Louis Collins, “Multi-contrast unbiased MRI atlas of a Parkinson's disease population,” International Journal of Computer-Assisted Radiology and Surgery, vol. 10(3), pp. 329-341, 2015.

3.Y. Xiao, V. Fonov, S. Beriault, F.A. Subaie, M.M. Chakravarty, A.F. Sadikot, G. Bruce Pike, and D. Louis Collins, “A dataset of multi-contrast population-averaged brain MRI atlases of a Parkinson’s disease cohort,”Data in Brief, 2017.

When using the downsamled BigBrain atlases, please cite the following article:
1. Amunts, K. et al.: “BigBrain: An Ultrahigh-Resolution 3D Human Brain Model”, Science (2013) 340 no. 6139 1472-1475, June 2013