Brain/MINDS Marmoset Brain MRI Dataset NA216 (In Vivo) and eNA91 (Ex Vivo)

Dataset Description :

The Brain/MINDS Marmoset MRI NA216 and eNA91 datasets currently constitutes the largest public marmoset brain MRI resource (483 individuals), and includes in vivo and ex vivo data for large variety of image modalities covering a wide age range of marmoset subjects.

  • The in vivo part corresponds to a total of 455 individuals, ranging in age from 0.6 to 12.7 years (mean age: 3.86 ± 2.63), and standard brain data (NA216) from 216 of these individuals (mean age: 4.46 ± 2.62).
    T1WI, T2WI, T1WI/T2WI, DTI metrics (FA, FAc, MD, RD, AD), DWI, rs-fMRI in awake and anesthetized states, NIfTI files (.nii.gz) of label data, individual brain and population average connectome matrix (structural and functional) csv files are included.
  • The ex vivo part is ex vivo data, mainly from a subset of 91 individuals with a mean age of 5.27 ± 2.39 years.
    It includes NIfTI files (.nii.gz) of standard brain, T2WI, DTI metrics (FA, FAc, MD, RD, AD), DWI, and label data, and csv files of individual brain and population average structural connectome matrices.

Imaging Method :

The detailed imaging methods for NA216 and eNA91 are available here.

Usage Notes :

  • A description of the region names for individual lines and columns of the SC and FC matrices can be found here.
  • For the purpose of online previews, original data have been preprocessed and formatted for optimized display. E.g. for most Nifti files, contrast enhancement of the data was performed to improve visibility. The resolution across in vivo and ex vivo was standardized and bit-depth reduction (to 8-bits) on the majority of data was used to reduce loading times.
  • Some web browsers (e.g. Safari) might display CSV files in a new tab when clicking on the download button. In that case, the file can either be saved from the newly opened tab (shortcut: [Command]+S), or directly downloaded using [Ctrl]+click on the download button and selecting “Download linked file”.

Citation :

Junichi Hata, Ken Nakae, Daisuke Yoshimaru, Hideyuki Okano. Brain/MINDS Marmoset Brain MRI Dataset NA216 and eNA91: (DataID: 4624)

License :

Related Publications :

  • 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, Hiro Taiyo Hamada, Carlos Enrique Gutierrez, Henrik Skibbe, Masahide Maeda, Frederic Papazian, Kei Hagiya, Noriyuki Kishi, Shin Ishii, Kenji Doya, Tomomi Shimogori, Tetsuo Yamamori, Keiji Tanaka, Hirotaka James Okano & Hideyuki Okano.
    Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range. Nature Scientific Data 10, 221 (2023).
  • Kanako Muta, Junichi Hata, Naoki Kawaguchi, Yawara Haga, Daisuke Yoshimaru, Kei Hagiya, Takaaki Kaneko, Takako Miyabe-Nishiwaki, Yuji Komaki, Fumiko Seki, Hirotaka James Okano & Hideyuki Okano.
    Effect of sedatives or anesthetics on the measurement of resting brain function in common marmosets.
    Cerebral cortex, 33(9), 5148–5162 (2023)
  • Yawara Haga, Junichi Hata, Akiko Uematsu, Fumiko Seki, Yuji Komaki, Mai Mizumura, Marin Nishio, Takaaki Kaneko, Noriyuki Kishi, Hideyuki Okano, Akira Furukawa.
    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.
  • 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)
  • Uematsu, A., Hata, J., Komaki, Y., Seki, F., Yamada, C., Okahara, N., Okahara., Kurotaki, Y., Sasaki E. & Okano, H.
    Mapping orbitofrontal-limbic maturation in non-human primates: A longitudinal magnetic resonance imaging study.
    NeuroImage 163, 55-67 (2017)

Contributors and Acknowledgements :

Laboratory for Marmoset Neural Architecture : Experiments, Image processing.

Connectome Analysis Unit : Viewer development, atlasing.

As part of Brain/MINDS project, this work was supported by Japan Agency for Medical Research and Development (AMED).

Data Download & Preview :

View dataset on Brain/MINDS GIN server , or retrieve it with
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Usage Examples
  • Inspect NIfTI brain data using Python (beginner's level) : Tutorial page.
  • Create a symmetric brain image from individual brain using image registration techniques (ANTs) : Tutorial page.