Spinal Cord Toolbox
{{refimprove|date=July 2016}}
{{Infobox software
| name = Spinal Cord Toolbox
| title =
| logo =
| screenshot =
| caption =
| collapsible =
| author =
| developer = NeuroPoly
| released =
| discontinued =
| latest release version = 3.0.3
| latest release date = {{Start date and age|2017|04|26|df=yes}}
| latest preview version =
| latest preview date =
| repo = {{URL|https://github.com/neuropoly/spinalcordtoolbox}}
| programming language = Python
| operating system = Linux, Mac OS X
| platform =
| size = 140 MB
| language = English
| status =
| genre = Digital imaging
| license = MIT Licence
}}
Spinal Cord Toolbox (SCT) De Leener B, Lévy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, et al. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data. Neuroimage. 2017;145: 24–43. doi:10.1016/j.neuroimage.2016.10.009 is a suite of analysis tools optimized for spinal cord images acquired with magnetic resonance imaging. Main features include segmentation, registration and calculation of anatomical metrics.
Features
- Propseg Automatic spinal cord segmentation.De Leener B, Cohen-Adad J, Kadoury S. Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling. Medical Imaging, IEEE Transactions on (in press). DOI: 10.1109/TMI.2015.2437192
- The PAM50 template is an anatomical template of the spinal cord that covers the full spinal cord and brainstem and is available for T1-, T2- and T2*-weighted MRI contrasts. The PAM50 template includes probabilistic segmentation of white matter, gray matter, CSF as well as probabilistic atlases of gray matter subregions and white matter pathways.Fonov V, Le Troter A, Taso M, De Leener B, Leveque G, Benhamou M, Sdika M, Benali H, Pradat PF, Collins DL, Callot V, Cohen-Adad J. Framework for integrated MRI average of the spinal cord white and gray matter: The MNI-Poly-AMU template. Neuroimage 2014. DOI: 10.1016/j.neuroimage.2014.08.057De Leener B, Fonov V, Collins DL, Callot V, Stikov N, Cohen-Adad J. PAM50: Multimodal template of the brainstem and spinal cord compatible with the ICBM152 space. Proceedings of the 25th Annual Meeting of ISMRM, Honolulu, USA. 2017. The template also include segmentation of spinal levels for automatic assessment of metrics at specific locations.Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Mikulis D, Fehlings MG. Resolving the anatomic variability of the human cervical spinal cord: a solution to facilitate advanced neural imaging. Proceedings of the 22nd Annual Meeting of ISMRM, Milan, Italy 2014:1719.
- A White Matter atlas including 29 partial volume masks of which matter tracts.Lévy S, Benhamou M, Naaman C, Rainville P, Callot V, Cohen-Adad J. White matter atlas of the human spinal cord with estimation of partial volume effect. Neuroimage. 2015;119: 262–271. doi:10.1016/j.neuroimage.2015.06.040