BMA 2019 Ex Vivo (Brain Space 2)
Authors: Alexander Woodward1*, Rui Gong1, Ken Nakae2, Junichi Hata3,4,5, Hideyuki Okano3,4, Shin Ishii2, Yoko Yamaguchi6,7,8
*corresponding author: Alexander Woodward (email@example.com)
This atlas is composed of a population average ex-vivo MRI T2WI contrast mapped with the BMA 2017 Ex Vivo (published by Woodward et al. The Brain/MINDS 3D digital marmoset brain atlas).
The population average MRI was constructed based on scans of 25 individual brains. The 25 brains were aligned with one another by iteratively applying linear and non-linear registration and averaging the transformation files until convergence. Data of individual brains were then resampled with an isotropic spatial resolution of 100×100×100µm3 and averaged across brain. The registration procedure gave a brain shape with a high signal-to-noise ratio compared to an individual MRI scan. The average MRI was then AC-PC aligned within an RAS (Right-Anterior-Superior) coordinate system.
Cortical flat map and mid-thickness surfaces for the left and right hemispheres are now provided in the common GIFTI format (*. gii) for surface data. These are compatible with Connectome Workbench (version 1.5.0 and higher) and a Scene file is also provided for easy viewing of the data.
Woodward, Alexander; Gong, Rui; Nakae, Ken; Hata, Junichi; Okano, Hideyuki; Ishii, Shin; Yamaguchi, Yoko : Brain/MINDS 3D Marmoset Reference Brain Atlas 2019 (DataID: 4520) https://doi.org/10.24475/bma.4520
Total downloads: 214
Population average ex-vivo MRI T2WI N=25
|labelmap/||sp2_label_512_3dslicer_v1.0.ctbl||Color look-up table|
Atlas region label map
|transforms/||sp1_to_sp2_affine_v1.0.txt||Linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Affine matrix.|
|sp1_to_sp2_invwarp_v1.0.nii.gz||Inverse of non-linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Displacement field.|
|sp1_to_sp2_warp_v1.0.nii.gz||Non-linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Displacement field.|
|bma_sp2_cortical_flatmaps_v1.0.0.zip||Flat map package||
Total downloads: 60
|bma_sp2.lh.cortex.label.gii||Left hemisphere cortex region label|
|bma_sp2.lh.flatmap.surf.gii||Left hemisphere cortical flat map|
|bma_sp2.lh.graymid.surf.gii||Left hemisphere cortical mid-thickness surface|
|bma_sp2.rh.cortex.label.gii||Right hemisphere cortex region label|
|bma_sp2.rh.flatmap.surf.gii||Right hemisphere cortical flat map|
|bma_sp2.rh.graymid.surf.gii||Right hemisphere cortical mid-thickness surface|
|bma_sp2_connectome_workbench.scene||Connectome workbench scene file|
|bma_sp2_connectome_workbench.spec||Connectome workbench specification file|
- 17-06-2021: Added Flat map package.
- 04-02-2020: Initial release.