SC#3 – SC templates, probabilistic atlases and postprocessing tools

Research Works

A few years ago, 3T morphometric studies led to the elaboration of a unique T2*-based SC MR template and associated SC probabilistic atlases of white and gray matter (named AMU15, followed by a refined version: AMU40) (available upon request).
These probabilistic WM/GM SC atlases have been integrated within the Spinal Cord Toolbox. All together, these templates provide a frame of reference for image registration and atlas-based MR quantification now widely used across the SC MR community. The AMU15 probabilistic atlases have also been used to feed the Spine Model for Safety and surgery (SM2s) (cf. iLab-Spine activities)

Based on the AMU40 MR template, automatic WM/GM segmentation has also been proposed. Thereby, a TBM (tensor based morphometry) analysis has highlighted some evidence of local GM atrophy occurring with age.

Thanks to very high spatial resolution (<200 um) obtained at ultra-high field (7T), new MR templates are now under investigation. Hence, the 7T SC AMU MP2RAGE-based template and subsequent parcellation has recently been proposed.

Taking advantage of very high resolution and new contrasts of 7T MR images, new models have been developed to segment the spinal cord and its structures (WM/GM), such as the seg_gm_sc_7t_t2star


Involved people: Virginie Callot, Arnaud Le Troter, Manuel Taso, Aurélien Massire, Samira Schinda, Nilser Laines Medina



Selected publications:

  1. Laines Medina N., C. Gros, J. Cohen-Adad, V. Callot, A. Le Troter, 2D Multi-Class Model for Gray and White Matter Segmentation of the cervical spinal cord at 7T, arXiv : 2110.06516, 2021,
  2. A. Massire, H. Rasoanandrianina, M. Guye, V. Callot, Anterior fissure, central canal, posterior septum and more: new insights into the cervical spinal cord gray and white matter regional organization using T1 mapping at 7T, Neuroimage, 2020, 205: 116275. doi: 10.1016/j.neuroimage.2019.116275
  3. De Leener, S. Lévy, V.S. Fonov, N. Stikov, L.D. Collins, V. Callot, J. Cohen-Adad SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data, Neuroimage, 2017, 145, 24-43
  4. De Leener, M. Taso, J. Cohen-Adad, V. Callot, Segmentation of the human spinal cord, « Special issue on tissue segmentation », MAGMA, Magn. Reson. Mater. Phy, 2016. doi: 10.1007/s10334-015-0507-2
  5. Taso, A. Le Troter, M. Sdika, J. Cohen-Adad, PJ. Arnoux, M. Guye, JP. Ranjeva, V. Callot, A reliable spatially normalized template of the human spinal cord – Applications to automated white matter/gray matter segmentation and Tensor-Based Morphometry (TBM) mapping of gray matter alterations occurring with age, Neuroimage, 2015, 117:20-8.doi: 10.1016/j.neuroimage.2015.05.034
  6. Taso, A. Le Troter, M. Sdika, JP. Ranjeva, M. Guye, M. Bernard, V. Callot, Construction of a Spinal Cord In Vivo Atlas based on high resolution MR images at cervical and thoracic levels : preliminary results, MAGMA, Magn. Reson. Mater. Phy, 27, 257-267; 2014. doi: 10.1007/s10334-013-0403-6


seg_gm_sc_7t_t2star : 2D Multi-Class Model for Gray and White Matter Segmentation of the Cervical Spinal Cord at 7T


7T SC WM/GM substructure parcellation derived from ultra high field MP2RAGE SC MR acquisitions (from Massive et al., Neuroimage 2020)


AMU15 SC WM/GM probabilistic atlases (from Taso et al., Magn. Reson. Mater. Phy, 2014)
SC WM/GM segmentation based on AMU40 – TBM analysis (from Taso et al., Neuroimage 2015)


Acknowledgments : we sincerely acknowledge grant supports from Fondation ARSEP (aide à la recherche sur la sclérose en plaques), NeuroAMUInstitut Marseille Imaging and ANR.

Associated Keywords

  • Image Processing
  • Image Segmentation
  • Spinal Cord
  • Ultra-high field MRI