61 lines
5.9 KiB
Markdown
61 lines
5.9 KiB
Markdown
# BMA 2019 Ex Vivo (Brain Space 2)
|
||
|
||
Authors: Alexander Woodward<sup>1</sup>*, Rui Gong<sup>1</sup>, Ken Nakae<sup>2</sup>, Junichi Hata<sup>3,4,5</sup>, Hideyuki Okano<sup>3,4</sup>, Shin Ishii<sup>2</sup>, Yoko Yamaguchi<sup>6,7,8</sup>
|
||
|
||
1. Connectome Analysis Unit, Integrative Computational Brain Science Collaboration Division, RIKEN Center for Brain Science
|
||
2. Integrated Systems Biology Laboratory (Ishii Laboratory), Division of Systems Informatics, Department of Systems Science, Graduate School of Informatics, Kyoto University
|
||
3. Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science
|
||
4. Department of Physiology (Okano Lab), Keio University School of Medicine, Keio University School of Medicine
|
||
5. Division of Regenerative Medicine, Jikei University School of Medicine
|
||
6. Applied Electronics Laboratory, Kanazawa Institute of Technology
|
||
7. Graduate School of Information Science and Technology, The University Tokyo
|
||
8. Laboratory for Cognitive Brain Mapping, RIKEN Center for Brain Science
|
||
|
||
*corresponding author: Alexander Woodward (alexander.woodward@riken.jp)
|
||
|
||
## DATASET DESCRIPTION
|
||
|
||
This atlas is composed of a population average ex-vivo MRI T2WI contrast mapped with the [BMA 2017 Ex Vivo](https://dataportal.brainminds.jp/reference-atlas-data/) (published by Woodward et al. [The Brain/MINDS 3D digital marmoset brain atlas](https://www.nature.com/articles/sdata20189)).
|
||
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](https://www.humanconnectome.org/software/connectome-workbench) (version 1.5.0 and higher) and a Scene file is also provided for easy viewing of the data.
|
||
KEYWORDS : digital atlas, marmoset, Callithrix jacchus, brain, reference atlas, 3D, NIfTI, brain atlas, 3D Slicer, flat map, GIfTI, Connectome Workbench
|
||
|
||
## CITATION
|
||
|
||
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
|
||
|
||
## LICENSE
|
||
|
||
This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
|
||
|
||
## CONTENT
|
||
|
||
| File name | Description |
|
||
| ---- | ---- |
|
||
|[`bma_2019_exvivo`](bma_2019_exvivo)/|Initial package|
|
||
|  [`CHANGES.txt`](bma_2019_exvivo/CHANGES.txt)|Change log|
|
||
|    [`base_data/`](bma_2019_exvivo/base_data/)||
|
||
|      [`sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz`](bma_2019_exvivo/base_data/sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz)|Population average ex-vivo MRI T2WI N=25|
|
||
|    [`labelmap/`](bma_2019_exvivo/labelmap/)||
|
||
|      [`sp2_label_512_3dslicer_v1.0.0.ctbl`](bma_2019_exvivo/labelmap/sp2_label_512_3dslicer_v1.0.0.ctbl)|Color look-up table|
|
||
|      [`sp2_label_512_v1.0.0.nii.gz`](bma_2019_exvivo/labelmap/sp2_label_512_v1.0.0.nii.gz)|Atlas region label map|
|
||
|    [`transforms/`](bma_2019_exvivo/transforms/)||
|
||
|      [`sp1_to_sp2_affine_v1.0.0.txt`](bma_2019_exvivo/transforms/sp1_to_sp2_affine_v1.0.0.txt)|Linear part of transformation between BMA 2017 (brain space 1) and BMA 2019 (brain space 2). Affine matrix.|
|
||
|      [`sp1_to_sp2_invwarp_v1.0.0.nii.gz`](bma_2019_exvivo/transforms/sp1_to_sp2_invwarp_v1.0.0.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_v1.0.0.nii.gz`](bma_2019_exvivo/transforms/sp1_to_sp2_warp_v1.0.0.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`](bma_sp2_cortical_flatmaps)|Flat map package|
|
||
|  [`CHANGES.txt`](bma_sp2_cortical_flatmaps/CHANGES.txt)|Change log|
|
||
|  [`bma_sp2.lh.cortex.label.gii`](bma_sp2_cortical_flatmaps/bma_sp2.lh.cortex.label.gii)|Left hemisphere cortex region label|
|
||
|  [`bma_sp2.lh.flatmap.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.lh.flatmap.surf.gii)|Left hemisphere cortical flat map|
|
||
|  [`bma_sp2.lh.graymid.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.lh.graymid.surf.gii)|Left hemisphere cortical mid-thickness surface|
|
||
|  [`bma_sp2.rh.cortex.label.gii`](bma_sp2_cortical_flatmaps/bma_sp2.rh.cortex.label.gii)|Right hemisphere cortex region label|
|
||
|  [`bma_sp2.rh.flatmap.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.rh.flatmap.surf.gii)|Right hemisphere cortical flat map|
|
||
|  [`bma_sp2.rh.graymid.surf.gii`](bma_sp2_cortical_flatmaps/bma_sp2.rh.graymid.surf.gii)|Right hemisphere cortical mid-thickness surface|
|
||
|  [`bma_sp2_connectome_workbench.scene`](bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.scene)|Connectome workbench scene file|
|
||
|  [`bma_sp2_connectome_workbench.spec`](bma_sp2_cortical_flatmaps/bma_sp2_connectome_workbench.spec)|Connectome workbench specification file|
|
||
|
||
## VERSION HISTORY
|
||
|
||
* 17-06-2021: Added Flat map package.
|
||
* 04-02-2020: Initial release.
|
||
|