This set of multi-contrast population-averaged PD brain atlas contains 5 different image contrasts:  T1w ( FLASH & MPRAGE), T2*w, T1–T2* fusion, phase, and an R2* map. Probabilistic tissue maps of whiter matter, grey matter, and cerebrospinal fluid are provided for the atlas. We also manually segmented eight subcortical structures: caudate nucleus, putamen, globus pallidus internus and externus (GPi & GPe), thalamus, STN, substantia nigra (SN), and the red nucleus (RN). Lastly, a co-registered histology-derived digitized atlas containing 123 anatomical structures is included.
We employed a novel T1–T2* fusion MRI that visualizes both cortical and subcortical structures to drive groupwise registration to create co-registered multi-contrast  unbiased templates from 25 PD patients that later went for the STN deep brain stimulation procedure. The finished atlas is in ICBM152 space. Three different resolutions are provided: 1×1×1 mm, 0.5×0.5×0.5 mm, and sectional 0.3×0.3×0.3 mm.

The included files are as followed:
R2* map: PD25-R2starmap-atlas-{0.3mm, 0.5mm, 1mm}
phase map: PD25-phase-atlas-{0.3mm, 0.5mm, 1mm}
MPRAGE T1: PD25-T1MPRAGE-template-{0.3mm, 0.5mm. 1mm}
FLASH T1: PD25-T1GRE-template-{0.3mm, 0.5mm, 1mm}
T2*w: PD25-T2star-template-{0.3mm, 0.5mm, 1mm}

T1-T2* fusion: PD25-fusion-template-{0.3mm, 0.5mm, 1mm}

Brain masks: PD25-atlas-mask-{0.3mm, 0.5mm, 1mm}
Probabilistic brain tissue maps: PD25-{WM,GM,CSF}-tissuemap
8 subcortical structure segmentation: PD25-subcortical-1mm
High resolution midbrain nuclei manual segmentation: PD25-midbrain-0.3mm

Co-registered histological atlas:  PD25-histo-{0.3mm, 1mm}

midbrain labels: PD25-midbrain-labels.csv
Subcortical labels: PD25-subcortical-labels.csv
Histological labels: PD25-histo-labels.csv

To facilitate the investigation of the neuroanatomy, the Big Brain atlas was nonlinearly registered to the contrast-enhanced T1-T2* fusion template. The registered results are available in 1×1×1 mm, 0.5×0.5×0.5 mm, sectional 0.3×0.3×0.3 mm, and whole brain 0.3×0.3×0.3 mm.
Screen Shot 2018-06-11 at 10.53.12 PM
Data related to Big Brain atlas registration:
Contrast enhanced T1-T2* fusion template: PD25-enhanceFusion-template-{0.3mm,0.5mm,1mm}
Co-registered Big Brain atlas: Bigbrain-to-PD25-{0.3mm,0.5mm,1mm}
Co-registered Big Brain atlas in global 0.3×0.3×0.3 mm: Bigbrain-to-PD25-global-300um
Nonlinear transformation from Big Brain in ICBM space to PD25: BigbrainICBM-to-PD25_nonlin.xfm


For the methods used, and to use the atlas for research purposes, please cite the following articles:
  1. 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,” accepted in Data in Brief, 2017.
  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, S. Beriault, G. Bruce Pike, and D. Louis Collins, “Multicontrast multiecho FLASH MRI for targeting the subthalamic nucleus,” Magnetic Resonance Imaging, vol. 30, pp. 627-640, 2012.

If you are using the Big Brain data, please cite the following publication:

  1. Amunts, K. et al.: “BigBrain: An Ultrahigh-Resolution 3D Human Brain Model”, Science (2013) 340 no. 6139 1472-1475, June 2013


Copyright (C) 2016,2017,2018 Yiming Xiao, McConnell Brain Imaging Centre,
Montreal Neurological Institute, McGill University.


Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported


Version 20170213: Download archives containing brain atlases, brain masks, midbrain and subcortical segmentation and histological labels: MINC1, MINC2, NIFTI

Version 20160706: Download archives containing brain atlases, brain masks and midbrain segmentation: MINC1, MINC2, NIFTI

Big brain data registration: Download archives containing contrast-enhanced T1-T2* fusion template, registered Big Brain atlas, and registration transformation: MINC2, NIFTI