In vivo DTI tractography of the rat brain: An atlas of the main tracts in Paxinos space with histological comparison

Matteo Figini, Ileana Zucca, Domenico Aquino, Paolo Pennacchio, Simone Nava, Alessandro Di Marzio, Maria Giulia Preti, Guseppe Baselli, Roberto Spreafico, Carolina Frassoni

Research output: Contribution to journalArticlepeer-review


Diffusion tensor imaging (DTI) is a magnetic resonance modality that permits to characterize the orientation and integrity of white matter (WM). DTI-based tractography techniques, allowing the virtual reconstruction of WM tract pathways, have found wide application in preclinical neurological research. Recently, anatomically detailed rat brain atlases including DTI data were constructed from ex vivo DTI images, but tractographic atlases of normal rats in vivo are still lacking. We propose here a probabilistic tractographic atlas of the main WM tracts in the healthy rat brain based on in vivo DTI acquisition. Our study was carried out on 10 adult female Sprague-Dawley rats using a 7. T preclinical scanner. The MRI protocol permitted a reliable reconstruction of the main rat brain bundles: corpus callosum, cingulum, external capsule, internal capsule, anterior commissure, optic tract. The reconstructed fibers were compared with histological data, proving the viability of in vivo DTI tractography in the rat brain with the proposed acquisition and processing protocol. All the data were registered to a rat brain template in the coordinate system of the commonly used atlas by Paxinos and Watson; then the individual tracts were binarized and averaged, obtaining a probabilistic atlas in Paxinos-Watson space of the main rat brain WM bundles. With respect to the recent high-resolution MRI atlases, the resulting tractographic atlas, available online, provides complementary information about the average anatomical position of the considered WM tracts and their variability between normal animals. Furthermore, reference values for the main DTI-derived parameters, mean diffusivity and fractional anisotropy, were provided. Both these results can be used as references in preclinical studies on pathological rat models involving potential alterations of WM.

Original languageEnglish
Pages (from-to)296-303
Number of pages8
JournalMagnetic Resonance Imaging
Issue number3
Publication statusPublished - Apr 1 2015


  • DTI
  • Histology
  • MRI
  • Rat brain
  • Tractographic atlas

ASJC Scopus subject areas

  • Biophysics
  • Radiology Nuclear Medicine and imaging
  • Biomedical Engineering
  • Medicine(all)


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