An in vivo MRI template set for morphometry, tissue segmentation, and fMRI localization in rats

Pedro Antonio Valdés-Hernández, Akira Sumiyoshi, Hiroi Nonaka, Risa Haga, Eduardo Aubert-Vásquez, Takeshi Ogawa, Yasser Iturria-Medina, Jorge J. Riera, Ryuta Kawashima

Research output: Contribution to journalArticlepeer-review

144 Citations (Scopus)


Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies.

Original languageEnglish
Article number26
JournalFrontiers in Neuroinformatics
Publication statusPublished - 2011 Nov 24


  • Anatomical connectivity
  • Elastix
  • FMRI
  • Morphometry
  • Paxinos and Watson
  • SPM
  • Template set
  • Wistar rats

ASJC Scopus subject areas

  • Neuroscience (miscellaneous)
  • Biomedical Engineering
  • Computer Science Applications


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