RESEARCH ARTICLE 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 • Michae ¨l Sdika • Jean-Philippe Ranjeva • Maxime Guye • Monique Bernard • Virginie Callot Received: 27 May 2013 / Revised: 9 July 2013 / Accepted: 14 August 2013 / Published online: 20 September 2013 Ó ESMRMB 2013 Abstract Object 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 vol- unteers using a multi-echo–gradient-echo sequence (1 slice per vertebral level from C1 to L2). After manual seg- mentation, linear and affine co-registrations were per- formed providing either inter-individual morphometric variability maps, or substructure probabilistic maps [CSF, white and grey matter (WM/GM)] and anatomical SC template. Results The larger inter-individual morphometric varia- tions 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. Conclusion 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 biome- chanical models usually based on post-mortem or generic data. Further work will consider integration into an auto- mated SC segmentation pipeline. Keywords MRI  Spinal cord  Morphology  Atlas  Spinal cord template Introduction Although challenging, spinal cord (SC) MRI has become widely investigated in both clinical and research studies of various pathologies including multiple sclerosis, myelopa- thy, trauma or syringomyelia. In order to enhance the overall knowledge of the spinal cord and its affections, parametrical analysis of multimodal MRI and group studies are conducted and segmentation algorithms are being developed to facili- tate analysis of these data within a common space. Current segmentation methods usually rely on T1- or T2-w images [1, 2], which provide optimal delineation of the cord but limited contrast to discriminate white and grey matter sub- structures. To achieve this deeper analysis, other strategies based on diffusion tensor imaging (DTI) [3] or highly con- trasted MRI [4] have proven to be useful, but these methods are currently limited to the cervical spinal cord. In this work, we propose a probabilistic spinal cord atlas built from in vivo, high-resolution axial T2*-w images acquired on healthy subjects along the entire spinal cord and M. Taso  A. Le Troter  J.-P. Ranjeva  M. Guye  M. Bernard  V. Callot (&) Centre de Re ´sonance Magne ´tique Biologique et Me ´dicale (CRMBM), UMR 7339, CNRS, Aix-Marseille Universite ´, 27, boulevard Jean Moulin, 13385 Marseille Cedex 05, France e-mail: virginie.callot@univ-amu.fr M. Taso e-mail: manuel.taso@gmail.com M. Sdika CREATIS, CNRS, UMR 5220, Inserm U1044, INSA-Lyon, Universite ´ Lyon 1, Universite ´ de Lyon, Lyon, France M. Guye APHM, CEMEREM, Ho ˆpitaux de la Timone, 13385 Marseille, France 123 Magn Reson Mater Phy (2014) 27:257–267 DOI 10.1007/s10334-013-0403-6