Construction of an in vivo human spinal cord atlas based on high-resolution MR images at cervical and thoracic levels: preliminary results

  • Manuel Taso
  • Arnaud Le Troter
  • Michaël Sdika
  • Jean-Philippe Ranjeva
  • Maxime Guye
  • Monique Bernard
  • Virginie CallotEmail author
Research Article



Our goal was to build a probabilistic atlas and anatomical template of the human cervical and thoracic spinal cord (SC) that could be used for segmentation algorithm improvement, parametric group studies, and enrichment of biomechanical modelling.

Materials and methods

High-resolution axial T2*-weighted images were acquired at 3T on 15 healthy volunteers using a multi-echo–gradient-echo sequence (1 slice per vertebral level from C1 to L2). After manual segmentation, linear and affine co-registrations were performed providing either inter-individual morphometric variability maps, or substructure probabilistic maps [CSF, white and grey matter (WM/GM)] and anatomical SC template.


The larger inter-individual morphometric variations were observed at the thoraco-lumbar levels and in the posterior GM. Mean SC diameters were in agreement with the literature and higher than post-mortem measurements. A representative SC MR template was generated and values up to 90 and 100 % were observed on GM and WM-probability maps.


This work provides a probabilistic SC atlas and a template that could offer great potentialities for parametrical MRI analysis (DTI/MTR/fMRI) and group studies, similar to what has already been performed using a brain atlas. It also offers great perspective for biomechanical models usually based on post-mortem or generic data. Further work will consider integration into an automated SC segmentation pipeline.


MRI Spinal cord Morphology Atlas Spinal cord template 



This work was supported by the CNRS (Centre National de la Recherche Scientifique) and the ANR (Agence Nationale de la Recherche).


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Copyright information

© ESMRMB 2013

Authors and Affiliations

  • Manuel Taso
    • 1
  • Arnaud Le Troter
    • 1
  • Michaël Sdika
    • 2
  • Jean-Philippe Ranjeva
    • 1
  • Maxime Guye
    • 1
    • 3
  • Monique Bernard
    • 1
  • Virginie Callot
    • 1
    Email author
  1. 1.Centre de Résonance Magnétique Biologique et Médicale (CRMBM), UMR 7339, CNRSAix-Marseille UniversitéMarseille Cedex 05France
  2. 2.CREATIS, CNRS, UMR 5220, Inserm U1044, INSA-Lyon, Université Lyon 1Université de LyonLyonFrance
  3. 3.APHM, CEMEREMHôpitaux de la TimoneMarseilleFrance

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