SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data

  title={SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data},
  author={Benjamin De Leener and Simon L{\'e}vy and Sara M. Dupont and Vladimir S. Fonov and Nikola Stikov and D. Louis Collins and Virginie Callot and Julien Cohen-Adad},
Atlas-Based Quantification of DTI Measures in a Typically Developing Pediatric Spinal Cord
The proposed automated pipeline incorporates unique postprocessing steps followed by template registration and quantification of DTI metrics using atlas-based regions and eliminates the need for manual ROI analysis of WM tracts and, therefore, increases the accuracy and speed of the measurements.
Quantitative magnetic resonance imaging of spinal cord microstructure in adults with cerebral palsy
  • J. Cohen-Adad
  • Medicine
    Developmental medicine and child neurology
  • 2021
The study aims to validate the relevance of magnetization transfer ratio and diffusion tensor imaging, both magnetic resonance imaging techniques, to quantify microstructural abnormalities in the spinal cord of adult patients with CP and demonstrates an association between these morphometric biomarkers and clinical scores of hand dexterity.
Generic acquisition protocol for quantitative MRI of the spinal cord.
The protocol will serve as a starting point for researchers and clinicians implementing new SC imaging initiatives so that, in the future, inclusion of the SC in neuroimaging protocols will be more common.
Diffusion Kurtosis Imaging of the neonatal Spinal Cord: design and application of the first processing pipeline implemented in Spinal Cord Toolbox
This work illustrates the first semi-automated pipeline for handling with DKI data of neonatal SC, from acquisition setting to estimation of diffusion (DTI & DKI) measures, through accurate adjustment of processing algorithms customized for adult SC, confirming validity of adopted pipeline and diagnostic value of DKI in pediatrics.
Effectiveness of regional diffusion MRI measures in distinguishing multiple sclerosis abnormalities within the cervical spinal cord
Average diffusion MRI metrics are extracted from the diffusion tensor imaging and Ball-and-Stick models and quantified for every cervical vertebral level using a collection of image processing methods and an atlas-based approach to characterize the feasibility of these metrics to detect lesions.
Cervical Spinal Cord Atrophy can be Accurately Quantified Using Head Images
C1 cross-sectional area calculated from brain imaging as a surrogate for the traditional C2/3 cross-section area measure for spinal cord atrophy is supported.
Mapping pediatric spinal cord development with age
Observing the growth of cord matter by patient age and vertebral level suggests that the upper cervical spinal cord, specifically C2-C3, and mid-thoracic spinal Cord, T3-T8, grow faster than other cervical levels and thoracic levels, respectively.
Generative diffeomorphic atlas construction from brain and spinal cord MRI data
The aim of the work is to explore how a hierarchical generative model of imaging data can serve to quantitatively investigate, in vivo, the morphology of the central nervous system (CNS).


Groupwise multi-atlas segmentation of the spinal cord's internal structure
Spinal Cord fMRI
Segmentation of the human spinal cord
It is concluded that robust and automatic segmentation is clinically relevant, as it would allow for longitudinal and group studies free from user bias as well as reproducible multicentric studies in large populations, thereby helping to further the understanding of the spinal cord pathophysiology.
Quantitative MRI of the Spinal Cord
Automatic Segmentation of the Spinal Cord and Spinal Canal Coupled With Vertebral Labeling
This paper presents a new framework combining PropSeg and a vertebral level identification method, thereby enabling direct inter- and intra-subject comparison of SC measurements for large cohort studies as well as for longitudinal studies.
Spinal cord spectroscopy and diffusion-based tractography to assess acute disability in multiple sclerosis.
MR spectroscopy and diffusion-based tractography of the cervical cord provide measures that are sensitive to the tissue damage occurring in this area in patients with a cervical cord relapse, and these measures were found to correlate with acute disability.