47 lines
3.1 KiB
Markdown
47 lines
3.1 KiB
Markdown
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# BMA 2017 Ex Vivo (Brain Space 1)
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Authors: Alexander Woodward<sup>1</sup>*, Tsutomu Hashikawa<sup>1,2</sup>, Masahide Maeda<sup>1</sup>, Takaaki Kaneko<sup>3</sup>, Keigo Hikishima<sup>4</sup>, Atsushi Iriki<sup>2</sup>, Hideyuki Okano<sup>3</sup>, Yoko Yamaguchi<sup>1</sup>*
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1. Neuroinformatics Japan Center, RIKEN Brain Science Institute
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2. Laboratory for Symbolic Cognitive Development, RIKEN Brain Science Institute
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3. Laboratory for Marmoset Neural Architecture, RIKEN Brain Science Institute
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4. Animal Resources Section, Okinawa Institute of Science and Technology Graduate University
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*corresponding authors: Alexander Woodward (alexander.woodward@riken.jp), Yoko Yamaguchi (yokoy@brain.riken.jp)
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## DATASET DESCRIPTION
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The dataset includes NIfTI files of MRI T2 ex-vivo data; reconstructed Nissl stained images of the same brain, registered to the shape of the MRI; brain region segmentation (with separate color lookup table); and gray, mid-cortical and white matter boundary segmentation. In addition, a 3D Slicer scene file is provided that can be used for testing the dataset within the freely downloadable 3D Slicer software (https://www.slicer.org/). The scene file can be dragged directly into 3D Slicer and the atlas can be used immediately. Files can be downloaded individually or as one zip file.
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The atlas can be viewed online via the Zooming Atlas Viewer (ZAV) by clicking here.
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KEYWORDS : digital atlas, marmoset, Callithrix jacchus, brain, reference atlas, 3D, NIfTI, brain atlas, 3D Slicer
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## CITATION
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Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko : Brain/MINDS 3D Marmoset Reference Brain Atlas 2017 (DataID: 2799) https://doi.org/10.24475/bma.2799
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## RELATED PUBLICATION(S)
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The technical details of the data and its generation is available in the following article:
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Woodward, Alexander; Hashikawa, Tsutomu; Maeda, Masahide; Kaneko, Takaaki; Hikishima, Keigo; Iriki, Atsushi; Okano, Hideyuki; Yamaguchi, Yoko (2017): The Brain/MINDS 3D digital marmoset brain atlas. https://www.nature.com/articles/sdata20189
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## CONTENT
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| File name | Description |
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| ---- | ---- |
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| [`bma-1-mri.nii.gz`](bma-1-mri.nii.gz) | MRI T2 ex-vivo volume (NIfTI-1) |
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| [`bma-1-nissl.nii.gz`](bma-1-nissl.nii.gz) | Nissl volume registered to MRI (NIfTI-1) |
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| [`bma-1-region_seg.nii.gz`](bma-1-region_seg.nii.gz) | Brain region segmentation volume (NIfTI-1) |
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| [`bma-1-graywhite_seg.nii.gz`](bma-1-graywhite_seg.nii.gz) | Gray and white matter boundary segmentation volume (NIfTI-1) |
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| [`bma-1-mid_seg.nii.gz`](bma-1-mid_seg.nii.gz) | Mid-cortical boundary segmentation volume (NIfTI-1) |
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| [`bma-1-clut.ctbl`](bma-1-clut.ctbl) | Color lookup table for bma-1-regionseg.nii (CTBL) |
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| [`bma-1-slicerscene.mrml`](bma-1-slicerscene.mrml) | 3D Slicer scene file (MRML) |
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| [`bma-1-mri_unprocessed_exvivo_t2wi.nii.gz`](bma-1-mri_unprocessed_exvivo_t2wi.nii.gz) | Unprocessed MRI T2WI ex-vivo volume with skull (NIfTI-1) |
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## VERSION HISTORY
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* 22-04-2020 - Updated. Unprocessed MRI T2WI ex-vivo volume with skull was added.
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* 22-11-2017 - Initial release.
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