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# Spinal Cord Toolbox [![Build Status](https://travis-ci.org/neuropoly/spinalcordtoolbox.svg?branch=master)](https://travis-ci.org/neuropoly/spinalcordtoolbox)


Comprehensive and open-source library of analysis tools for MRI of the spinal cord.

- [Installation](https://sourceforge.net/p/spinalcordtoolbox/wiki/installation/)
- [List of tools](http://sourceforge.net/p/spinalcordtoolbox/wiki/tools/)
- [Getting started](https://github.com/neuropoly/spinalcordtoolbox/blob/master/batch_processing.sh)
- [List of changes](https://github.com/neuropoly/spinalcordtoolbox/blob/master/CHANGES.md)

## References

#### Spinal Cord Toolbox
- [Cohen-Adad et al. Spinal Cord Toolbox: an open-source framework for processing spinal cord MRI data. Proceedings of the 20th Annual Meeting of OHBM, Hamburg, Germany 2014:3633](https://dl.dropboxusercontent.com/u/20592661/publications/cohenadad_ohbm14_spinalcordtoolbox.pdf)

#### Propseg
- [De Leener et al. Robust, accurate and fast automatic segmentation of the spinal cord. Neuroimage 2014;98:528-536.](https://dl.dropboxusercontent.com/u/20592661/publications/DeLeener_NIMG14_PropSeg.pdf)
- [Ullmann et al. Automatic labeling of vertebral levels using a robust template-based approach. Int J Biomed Imaging 2014;Article ID 719520.](http://downloads.hindawi.com/journals/ijbi/2014/719520.pdf)
- [De Leener et al. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. IEEE Transactions on Medical Imaging 2015; in press](https://www.dropbox.com/s/2tsp1juxcvuq4bl/PID3727605.pdf)

#### Template and Atlas
- [Fonov et al. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014;102P2:817-827.](https://dl.dropboxusercontent.com/u/20592661/publications/Fonov_NIMG14_MNI-Poly-AMU.pdf)
- [Taso et al. Construction of an in vivo human spinal cord atlas based on high-resolution MR images at cervical and thoracic levels: preliminary results. MAGMA, Magn Reson Mater Phy 2014;27(3):257-267](https://dl.dropboxusercontent.com/u/20592661/publications/taso_magma_2014.pdf)
- [Benhamou et al. Atlas of white-matter tracts in the human spinal cord. Proc. ISMRM, Milan, Italy 2014:5132](https://dl.dropboxusercontent.com/u/20592661/publications/benhamou_irmsm14.pdf)
- [Cadotte et al. Characterizing the Location of Spinal and Vertebral Levels in the Human Cervical Spinal Cord. AJNR Am J Neuroradiol 2014;(in press).](https://dl.dropboxusercontent.com/u/20592661/publications/Cadotte_AJNR14_SpinalLevel.pdf)
- [Touati et al. T1 and T2 template of the brainstem and spinal cord. Proc. ISMRM, Toronto, Canada 2015](https://www.dropbox.com/s/i7at66hugucrs1h/touati_ismrm15_template.pdf)

#### Registration
- [De Leener et al. Template-based analysis of multi-parametric MRI data with the Spinal Cord Toolbox. Proc. ISMRM, Toronto, Canada 2015](https://dl.dropboxusercontent.com/u/20592661/publications/deleener_ismrm15_sct.pdf) 
- [Cohen-Adad et al. Slice-by-slice regularized registration for spinal cord MRI: SliceReg. Proc. ISMRM, Toronto, Canada 2015](https://dl.dropboxusercontent.com/u/20592661/publications/cohenadad_ismrm15_slicereg.pdf)

## License
<commit_msg>added abstract on SCT from ISMRM<commit_after>
# Spinal Cord Toolbox [![Build Status](https://travis-ci.org/neuropoly/spinalcordtoolbox.svg?branch=master)](https://travis-ci.org/neuropoly/spinalcordtoolbox)


Comprehensive and open-source library of analysis tools for MRI of the spinal cord.

- [Installation](https://sourceforge.net/p/spinalcordtoolbox/wiki/installation/)
- [List of tools](http://sourceforge.net/p/spinalcordtoolbox/wiki/tools/)
- [Getting started](https://github.com/neuropoly/spinalcordtoolbox/blob/master/batch_processing.sh)
- [List of changes](https://github.com/neuropoly/spinalcordtoolbox/blob/master/CHANGES.md)

## References

#### Spinal Cord Toolbox
- [Cohen-Adad et al. Spinal Cord Toolbox: an open-source framework for processing spinal cord MRI data. Proceedings of the 20th Annual Meeting of OHBM, Hamburg, Germany 2014:3633](https://dl.dropboxusercontent.com/u/20592661/publications/cohenadad_ohbm14_spinalcordtoolbox.pdf)
- [De Leener et al. Template-based analysis of multi-parametric MRI data with the Spinal Cord Toolbox. Proc. ISMRM, Toronto, Canada 2015](https://www.dropbox.com/s/1gv81xg17lgcxfn/5798_submitted_radC862D.pdf)

#### Propseg
- [De Leener et al. Robust, accurate and fast automatic segmentation of the spinal cord. Neuroimage 2014;98:528-536.](https://dl.dropboxusercontent.com/u/20592661/publications/DeLeener_NIMG14_PropSeg.pdf)
- [Ullmann et al. Automatic labeling of vertebral levels using a robust template-based approach. Int J Biomed Imaging 2014;Article ID 719520.](http://downloads.hindawi.com/journals/ijbi/2014/719520.pdf)
- [De Leener et al. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. IEEE Transactions on Medical Imaging 2015; in press](https://www.dropbox.com/s/2tsp1juxcvuq4bl/PID3727605.pdf)

#### Template and Atlas
- [Fonov et al. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014;102P2:817-827.](https://dl.dropboxusercontent.com/u/20592661/publications/Fonov_NIMG14_MNI-Poly-AMU.pdf)
- [Taso et al. Construction of an in vivo human spinal cord atlas based on high-resolution MR images at cervical and thoracic levels: preliminary results. MAGMA, Magn Reson Mater Phy 2014;27(3):257-267](https://dl.dropboxusercontent.com/u/20592661/publications/taso_magma_2014.pdf)
- [Benhamou et al. Atlas of white-matter tracts in the human spinal cord. Proc. ISMRM, Milan, Italy 2014:5132](https://dl.dropboxusercontent.com/u/20592661/publications/benhamou_irmsm14.pdf)
- [Cadotte et al. Characterizing the Location of Spinal and Vertebral Levels in the Human Cervical Spinal Cord. AJNR Am J Neuroradiol 2014;(in press).](https://dl.dropboxusercontent.com/u/20592661/publications/Cadotte_AJNR14_SpinalLevel.pdf)
- [Touati et al. T1 and T2 template of the brainstem and spinal cord. Proc. ISMRM, Toronto, Canada 2015](https://www.dropbox.com/s/i7at66hugucrs1h/touati_ismrm15_template.pdf)

#### Registration
- [De Leener et al. Template-based analysis of multi-parametric MRI data with the Spinal Cord Toolbox. Proc. ISMRM, Toronto, Canada 2015](https://dl.dropboxusercontent.com/u/20592661/publications/deleener_ismrm15_sct.pdf) 
- [Cohen-Adad et al. Slice-by-slice regularized registration for spinal cord MRI: SliceReg. Proc. ISMRM, Toronto, Canada 2015](https://dl.dropboxusercontent.com/u/20592661/publications/cohenadad_ismrm15_slicereg.pdf)

## License

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