From 529edb5f9918f3a22b32beaa3f51657f6d825f03 Mon Sep 17 00:00:00 2001 From: brainminds Date: Wed, 12 Jul 2017 00:00:00 +0900 Subject: [PATCH] initial release --- .gitattributes | 2 + 12months/12mo_T1_Template_brain.nii.gz | 1 + 12months/12mo_T1_Template_head.nii.gz | 1 + 12months/12mo_T2_Template_brain.nii.gz | 1 + 12months/12mo_T2_Template_head.nii.gz | 1 + 18months/18mo_T1_Template_brain.nii.gz | 1 + 18months/18mo_T1_Template_head.nii.gz | 1 + 18months/18mo_T2_Template_brain.nii.gz | 1 + 18months/18mo_T2_Template_head.nii.gz | 1 + 1month/1mo_T1_Template_brain.nii.gz | 1 + 1month/1mo_T1_Template_head.nii.gz | 1 + 1month/1mo_T2_Template_brain.nii.gz | 1 + 1month/1mo_T2_Template_head.nii.gz | 1 + 24months/24mo_T1_Template_brain.nii.gz | 1 + 24months/24mo_T1_Template_head.nii.gz | 1 + 24months/24mo_T2_Template_brain.nii.gz | 1 + 24months/24mo_T2_Template_head.nii.gz | 1 + 3months/3mo_T1_Template_brain.nii.gz | 1 + 3months/3mo_T1_Template_head.nii.gz | 1 + 3months/3mo_T2_Template_brain.nii.gz | 1 + 3months/3mo_T2_Template_head.nii.gz | 1 + 6months/6mo_T1_Template_brain.nii.gz | 1 + 6months/6mo_T1_Template_head.nii.gz | 1 + 6months/6mo_T2_Template_brain.nii.gz | 1 + 6months/6mo_T2_Template_head.nii.gz | 1 + Additional_information_about_the_dataset.pdf | 1 + LICENSE | 403 +++++++++++++++++++ README.md | 46 +++ 28 files changed, 476 insertions(+) create mode 120000 12months/12mo_T1_Template_brain.nii.gz create mode 120000 12months/12mo_T1_Template_head.nii.gz create mode 120000 12months/12mo_T2_Template_brain.nii.gz create mode 120000 12months/12mo_T2_Template_head.nii.gz create mode 120000 18months/18mo_T1_Template_brain.nii.gz create mode 120000 18months/18mo_T1_Template_head.nii.gz create mode 120000 18months/18mo_T2_Template_brain.nii.gz create mode 120000 18months/18mo_T2_Template_head.nii.gz create mode 120000 1month/1mo_T1_Template_brain.nii.gz create mode 120000 1month/1mo_T1_Template_head.nii.gz create mode 120000 1month/1mo_T2_Template_brain.nii.gz create mode 120000 1month/1mo_T2_Template_head.nii.gz create mode 120000 24months/24mo_T1_Template_brain.nii.gz create mode 120000 24months/24mo_T1_Template_head.nii.gz create mode 120000 24months/24mo_T2_Template_brain.nii.gz create mode 120000 24months/24mo_T2_Template_head.nii.gz create mode 120000 3months/3mo_T1_Template_brain.nii.gz create mode 120000 3months/3mo_T1_Template_head.nii.gz create mode 120000 3months/3mo_T2_Template_brain.nii.gz create mode 120000 3months/3mo_T2_Template_head.nii.gz create mode 120000 6months/6mo_T1_Template_brain.nii.gz create mode 120000 6months/6mo_T1_Template_head.nii.gz create mode 120000 6months/6mo_T2_Template_brain.nii.gz create mode 120000 6months/6mo_T2_Template_head.nii.gz create mode 120000 Additional_information_about_the_dataset.pdf create mode 100644 LICENSE create mode 100644 README.md diff --git a/.gitattributes b/.gitattributes index af926ef..f866fed 100644 --- a/.gitattributes +++ b/.gitattributes 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For +the avoidance of doubt, this paragraph does not form part of the +public licenses. + +Creative Commons may be contacted at creativecommons.org. + diff --git a/README.md b/README.md new file mode 100644 index 0000000..2f5d7b2 --- /dev/null +++ b/README.md @@ -0,0 +1,46 @@ +# Brain/MINDS Marmoset MRI developmental age-specific templates + +Authors: Fumiko Seki1,2,3, Keigo Hikishima1,2,4, Yuji Komaki1,2, Junichi Hata1,2,3, Akiko Uematsu1,2,3, Norio Okahara2, Masafumi Yamamoto2, Haruka Shinohara2, Erika Sasaki1,2, Hideyuki Okano1,3* + +1. Department of Physiology (Okano Lab), Keio University School of Medicine, Keio University School of Medicine +2. Central Institute for Experimental Animals +3. Laboratory for Marmoset Neural Architecture, RIKEN Brain Science Institute +4. Okinawa Institute of Science and Technology Graduate University + +*corresponding author: Hideyuki Okano (hidokano@a2.keio.jp) + +## DATASET DESCRIPTION + +The dataset includes NifTI files of MRI T1-weighted images data and T2-weighted images at the age of 1 month, 3 months, 6 months, 12 months, 18 months, and 24 months. The templates at the age of 18 and 24 months were registered to the stereotaxic coordinates defined in Paxinos**1** and Woodward et al**2**. For the template at the age of 1, 3, 6, 12 months, we newly defined the stereotaxic coordinates. For details regarding the procedure, please see [Additional_information_about_the_dataset](./Additional_information_about_the_dataset.pdf) + +* [**1**]: Paxinos G. _The marmoset brain in stereotaxic coordinates_. Academic Press. 2012. +* [**2**]: Woodward A, Hashikawa T, Maeda M, Kaneko T, Hikishima K, Iriki A, Okano H, Yamaguchi Y. _The Brain/MINDS 3D digital marmoset brain atlas_. +DOI: https://doi.org/10.24475/bma.2799 + +## CITATION + +Seki, Fumiko; Hikishima, Keigo; Komaki, Yuji; Hata, Junichi; Uematsu, Akiko; Okahara, Norio; Yamamoto, Masafumi; Shinohara, Haruka; Sasaki, Erika; Okano, Hideyuki : _Developmental Age-Specific Brain Templates Dataset (DataID: 3405)_ DOI: https://doi.org/10.24475/bminds.mri.kfs.3405 + +## RELATED PUBLICATION(S) + +Seki F, Hikishima K, Komaki Y, Hata J, Uematsu A, Okahara N, Yamamoto M, Shinohara H, Sasaki E, Okano H. _Developmental trajectories of macroanatomical structures in common marmoset brain_. Neuroscience, 364(19):143-156, 2017. +DOI: https://doi.org/10.1016/j.neuroscience.2017.09.021 + +Details of materials and methods about the template reconstruction are available there. + +## LICENSE + +This work is licensed under a [Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License](http://creativecommons.org/licenses/by-nc-nd/4.0/). + +## CONTENT + +| File name | Description | +| ---- | ---- | +|[`Additional_information_about_the_dataset.pdf`](Additional_information_about_the_dataset.pdf)|The details about the stereotaxic coordinates in developing brain | +|[`1month/`](1month/)|N=13 (male, 7; female, 6)| +|[`3months/`](3months/)|N=15 (male, 7; female, 8)| +|[`6months/`](6months/)|N=16 (male, 9; female, 7)| +|[`12months/`](12months/)|N=16 (male, 8; female, 8)| +|[`18months/`](18months/)|N=17 (male, 7 female, 10)| +|[`24months/`](24months/)|N=13 (male, 5; female, 8)| +