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

@article{Leener2017SCTSC,
  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},
  journal={NeuroImage},
  year={2017},
  volume={145},
  pages={24-43}
}
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References

SHOWING 1-10 OF 106 REFERENCES
Groupwise multi-atlas segmentation of the spinal cord's internal structure
Spinal Cord fMRI
Segmentation of the human spinal cord
TLDR
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
TLDR
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.
TLDR
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.
...
...