major update: add DWI & rs-fMRI data & new license
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README.md
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README.md
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# Brain/MINDS Marmoset Brain MRI Dataset NA216 (In Vivo) and eNA91 (Ex Vivo)
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Creators: Junichi Hata<sup>1,2,3,</sup>*, Daisuke Yoshimaru<sup>1,2</sup>, Hideyuki Okano<sup>1,2,</sup>*
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Creators: Junichi Hata<sup>1,2,3,</sup>\*, Ken Nakae<sup>4</sup>, Daisuke Yoshimaru<sup>1,2</sup>, Hideyuki Okano<sup>1,2,</sup>\*
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1. Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science
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2. Department of Physiology, Keio University School of Medicine
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3. Division of Regenerative Medicine, Jikei University School of Medicine
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4. Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences
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*corresponding creator: Hideyuki Okano (hidokano@a2.keio.jp), Junichi Hata (j-hata@tmu.ac.jp)
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## DATASET DESCRIPTION
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Brain/MINDS Marmoset MRI datasets NA216 and eNA91.
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The Brain/MINDS Marmoset MRI NA216 and eNA91 datasets currently constitutes the largest public marmoset brain MRI resource, and includes in vivo and ex vivo data for large variety of image modalities covering a wide age range of marmoset subjects.
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NA216, which were taken in vivo, includes NIfTI files (.nii.gz) of T1WI, T2WI, T1WI/T2WI, DTI metrics (FA, FAc, MD, RD, and AD), and label data, and csv files of connectome matrices (structural and functional), for individual brains and population average. They were mostly taken from 216 individuals with an average age of 4.46 ±2.62 years old.
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eNA91, which were taken ex vivo, includes NIfTI files (.nii.gz) of T2WI, DTI metrics (FA, FAc, MD, RD, and AD), and label data, and csv files of structural connectome matrix, for individual brains and population average. They were mostly taken from 91 individuals with an average age of 5.27 ±2.39 years old.
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* The NA216 part corresponds to in vivo data that were mostly taken from 216 individuals with an average age of 4.46 ±2.62 years.
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It includes NIfTI files (.nii.gz) of T1WI, T2WI, T1WI/T2WI, DTI metrics (FA, FAc, MD, RD, and AD), DWI, rs-fMRI in awake and anesthetized states, and label data, csv files of connectome matrices (structural and functional), for individual brains and population average.
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* The eNA91 part corresponds ex vivo data, mostly taken from a subset of 91 individuals with an average age of 5.27 ±2.39 years.
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It includes NIfTI files (.nii.gz) of T2WI, DTI metrics (FA, FAc, MD, RD, and AD), DWI, and label data, and csv files of structural connectome matrix, for individual brains and population average.
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## CITATION
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Junichi Hata, Ken Nakae, Hiromichi Tsukada, Alexander Woodward, Yawara Haga, Mayu Iida, Akiko Uematsu, Fumiko Seki, Noritaka Ichinohe, Rui Gong, Takaaki Kaneko, Daisuke Yoshimaru, Akiya Watakabe, Hiroshi Abe, Toshiki Tani, Henrik Skibbe, Masahide Maeda, Frederic Papazian, Kei Hagiya, Noriyuki Kishi, Tomomi Shimogori, Tetsuo Yamamori, Hirotaka James Okano, Hideyuki Okano.
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_Multi-modal magnetic resonance image database of marmoset brains_. bioRxiv 2022.09.21.508952;
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doi: https://doi.org/10.1101/2022.09.21.508952
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Junichi Hata, Ken Nakae, Daisuke Yoshimaru, Hideyuki Okano. _Brain/MINDS Marmoset Brain MRI Dataset NA216 and eNA91: (DataID: 4624)_
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doi: https://doi.org/10.24475/bminds.mri.thj.4624
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## RELATED PUBLICATION(S)
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* Junichi Hata, Ken Nakae, Hiromichi Tsukada, Alexander Woodward, Yawara Haga, Mayu Iida, Akiko Uematsu, Fumiko Seki, Noritaka Ichinohe, Rui Gong, Takaaki Kaneko, Daisuke Yoshimaru, Akiya Watakabe, Hiroshi Abe, Toshiki Tani, Henrik Skibbe, Masahide Maeda, Frederic Papazian, Kei Hagiya, Noriyuki Kishi, Tomomi Shimogori, Tetsuo Yamamori, Hirotaka James Okano, Hideyuki Okano.
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_Multi-modal magnetic resonance image database of marmoset brains_. bioRxiv 2022.09.21.508952;
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doi: https://doi.org/10.1101/2022.09.21.508952
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* Yawara Haga, Junichi Hata, Akiko Uematsu, Fumiko Seki, Yuji Komaki, Mai Mizumura, Marin Nishio, Takaaki Kaneko, Noriyuki Kishi, Hideyuki Okano, Akira Furukawa.
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_MR Imaging Properties of ex vivo Common Marmoset Brain after Formaldehyde Fixation_. Magnetic Resonance in Medical Sciences, 2019, Volume 18, Issue 4, Pages 253-259, Released October 15, 2019, [Advance publication] Released February 07, 2019, Online ISSN 1880-2206, Print ISSN 1347-3182,
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doi: https://doi.org/10.2463/mrms.mp.2018-0086
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@ -38,7 +44,7 @@ doi: https://doi.org/10.1016/j.neuroimage.2017.09.028
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## LICENSE
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This work is licensed under a [Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License](http://creativecommons.org/licenses/by-nc-nd/4.0/).
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This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/).
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## CONTENT
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@ -57,6 +63,10 @@ This work is licensed under a [Creative Commons Attribution-NonCommercial-NoDeri
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| [`i_DTI_MD/`](invivo/i_DTI_MD/)|Mean diffusivity (n=126, nifti format)|
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| [`i_DTI_FA`](invivo/i_DTI_FA)|Fractional anisotropy of diffusivity (n=126, nifti format)|
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| [`i_DTI_FAc/`](invivo/i_DTI_FAc/)|Color encoding of the axial direction with FA weighting (n=126, nifti format)|
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| [`i_DWI_raw/`](invivo/i_DWI_raw/)|Diffusion MRI raw data (n=126, nifti format)|
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| [`i_DWI_MPG_info/`](invivo/i_DWI_MPG_info/)|bvalue and bvector information of DWI MRI (text format)|
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| [`i_fMRI_Awake_raw/`](invivo/i_fMRI_Awake_raw/)|Original functional MRI in awake state (n=3, nifti format)|
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| [`i_fMRI_Aneth_raw/`](invivo/i_fMRI_Aneth_raw/)|Original functional MRI in anesthetized state (n=31, nifti format)|
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| [`i_Label006/`](invivo/i_Label006/)|Labeling 6 regions of gray matter (n=216, nifti format)|
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| [`i_Label052/`](invivo/i_Label052/)|Labeling 52 regions of gray matter (n=216, nifti format)|
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| [`i_Label111/`](invivo/i_Label111/)|Labeling 111 regions of gray matter (n=216, nifti format)|
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| [`i_AnethFC/`](invivo/i_AnethFC/)|Connectome matrix by anesthetized rs-fMRI (n=31, csv format)|
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| [`i_Variables_gm/`](invivo/i_Variables_gm/)|Averaged variables in individual gray matter regions (BMA 2019 mapped, xlsx format)|
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| [`i_Average/`](invivo/i_Average/)|Population average|
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| [`i_deformable_info/`](invivo/i_deformable_info/)|Transformation coordinate information for image to NA216|
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|[`exvivo/`](exvivo/)|All data about MRI in Exvivo (n=91)|
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| [`e_Individual_List/`](exvivo/e_Individual_List/)|Information of individual animals (xlsx format)|
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| [`e_T2WI/`](exvivo/e_T2WI/)|Contrast with emphasis on T2 relaxation (n=91, nifti format)|
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| [`e_DTI_MD/`](exvivo/e_DTI_MD/)|Mean diffusivity (n=50, nifti format)|
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| [`e_DTI_FA/`](exvivo/e_DTI_FA/)|Fractional anisotropy of diffusivity (n=50, nifti format)|
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| [`e_DTI_FAc/`](exvivo/e_DTI_FAc/)|Color encoding of the axial direction with FA weighting (n=50, nifti format)|
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| [`e_DWI_raw/`](exvivo/e_DWI_raw/)|Diffusion MRI raw data (n=50, nifti format)|
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| [`e_DWI_MPG_info/`](exvivo/e_DWI_MPG_info/)|bvalue and bvector information of DWI MRI (text format)|
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| [`e_Label052/`](exvivo/e_Label052/)|Labeling 52 regions of gray matter (n=50, nifti format)|
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| [`e_DiffusionSC/`](exvivo/e_DiffusionSC/)|Connectome matrix by diffusion tractography (n=50, csv format)|
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| [`e_Variables_gm/`](exvivo/e_Variables_gm/)|Averaged variables in individual gray matter regions (BMA 2019 mapped, xlsx format)|
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| [`e_Average/`](exvivo/e_Average/)|Population average|
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| [`e_deformable_info/`](exvivo/e_deformable_info/)|Transformation coordinate information for image to NA216|
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|[`bma2019_mapping/`](bma2019_mapping/)|Brain/MINDS Atlas 2019 Mappings|
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