Skip to content

Latest commit

 

History

History
110 lines (91 loc) · 7.15 KB

citing_sct.rst

File metadata and controls

110 lines (91 loc) · 7.15 KB
Raw

Citing SCT

If you use SCT in your research or as part of your developments, please always cite the main reference. If you use specific tools such as sct_deepseg_sc or the PAM50 template, please also cite the specific articles listed in specific references.

Main Reference

  • De Leener B, Levy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, Callot V, Cohen-Adad J. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage 2017. <https://www.ncbi.nlm.nih.gov/pubmed/27720818>__
@article{DeLeener201724,
title = "SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord \{MRI\} data ",
journal = "NeuroImage ",
volume = "145, Part A",
number = "",
pages = "24 - 43",
year = "2017",
note = "",
issn = "1053-8119",
doi = "https://doi.org/10.1016/j.neuroimage.2016.10.009",
url = "https://www.sciencedirect.com/science/article/pii/S1053811916305560",
author = "Benjamin De Leener and Simon Lévy and Sara M. Dupont and Vladimir S. Fonov and Nikola Stikov and D. Louis Collins and Virginie Callot and Julien Cohen-Adad",
keywords = "Spinal cord",
keywords = "MRI",
keywords = "Software",
keywords = "Template",
keywords = "Atlas",
keywords = "Open-source ",
}

Specific References

Command Line Tools

The table below provides individual references for novel methods used in SCT's command-line-tools.

Note

If you are using white matter/grey matter segmentation tools (sct_deepseg_gm/sct_deepseg) and registration tools (sct_register_to_template/sct_register_multimodal) together as part of a pipeline, please also consider this reference:

Dupont SM, De Leener B, Taso M, Le Troter A, Stikov N, Callot V, Cohen-Adad J. Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter. Neuroimage 2017

Command line script References
sct_deepseg_gm Perone et al. Spinal cord gray matter segmentation using deep dilated convolutions. Sci Rep 2018
sct_deepseg_lesion Gros et al. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage 2019
sct_deepseg_sc Gros et al. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage 2019
sct_get_centerline Gros et al. Automatic spinal cord localization, robust to MRI contrasts using global curve optimization. Med Image Anal 2018
sct_label_vertebrae Ullmann et al. Automatic labeling of vertebral levels using a robust template-based approach. Int J Biomed Imaging 2014
sct_process_segmentation -pmj Bédard S, Cohen-Adad J. Automatic measure and normalization of spinal cord cross-sectional area using the pontomedullary junction. Frontiers in Neuroimaging 2022
sct_process_segmentation -normalize Bédard S, Cohen-Adad J. Automatic measure and normalization of spinal cord cross-sectional area using the pontomedullary junction. Frontiers in Neuroimaging 2022
sct_propseg De Leener et al. Robust, accurate and fast automatic segmentation of the spinal cord. Neuroimage 2014
sct_propseg -CSF De Leener et al. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. IEEE Transactions on Medical Imaging 2015
sct_register_multimodal De Leener B, Fonov VS, Louis Collins D, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage 2017.
sct_register_multimodal --param algo=slicereg Cohen-Adad et al. Slice-by-slice regularized registration for spinal cord MRI: SliceReg. Proc ISMRM 2015
sct_register_to_template De Leener B, Fonov VS, Louis Collins D, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage 2017.
sct_register_to_template --param algo=slicereg Cohen-Adad et al. Slice-by-slice regularized registration for spinal cord MRI: SliceReg. Proc ISMRM 2015
sct_straighten_spinalcord De Leener B et al. Topologically-preserving straightening of spinal cord MRI. J Magn Reson Imaging 2017

Template and Atlas

The table below provides references relevant to the pam50 used by SCT, including a reference for the template itself, as well as earlier works that the template builds on.

Template/atlas References
PAM50 template De Leener B, Fonov VS, Louis Collins D, Callot V, Stikov N, Cohen-Adad J. PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space. Neuroimage 2018.
MNI-Poly-AMU template Fonov et al. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014.
White matter atlas Lévy et al. White matter atlas of the human spinal cord with estimation of partial volume effect. Neuroimage 2015
Probabilistic atlas (AMU40) Taso et al. 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
Spinal levels Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Wilson JR, Mikulis D, Nugaeva N, Fehlings MG. Characterizing the location of spinal and vertebral levels in the human cervical spinal cord. AJNR Am J Neuroradiol, 2015, 36(4):803-810.