Journal
NEUROIMAGE
Volume 145, Issue -, Pages 24-43Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.neuroimage.2016.10.009
Keywords
Spinal cord; MRI; Software; Template; Atlas; Open-source
Funding
- Canada Research Chair in Quantitative Magnetic Resonance Imaging
- Canadian Institute of Health Research [CIHR FDN-143263]
- Fonds de Recherche du Quebec - Sante [28826]
- Fonds de Recherche du Quebec - Nature et Technologies [2015-PR-182754]
- Natural Sciences and Engineering Research Council of Canada [435897-2013]
- Sensorimotor Rehabilitation Research Team (SMRRT)
- Functional Neuroimaging Unit (CRIUGM, Universite de Montreal)
- Quebec BioImaging Network
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For the past 25 years, the field of neuroimaging has witnessed the development of several software packages for processing multi-parametric magnetic resonance imaging (mpMRI) to study the brain. These software packages are now routinely used by researchers and clinicians, and have contributed to important breakthroughs for the understanding of brain anatomy and function. However, no software package exists to process mpMRI data of the spinal cord. Despite the numerous clinical needs for such advanced mpMRI protocols (multiple sclerosis, spinal cord injury, cervical spondylotic myelopathy, etc.), researchers have been developing specific tools that, while necessary, do not provide an integrative framework that is compatible with most usages and that is capable of reaching the community at large. This hinders cross-validation and the possibility to perform multi-center studies. In this study we introduce the Spinal Cord Toolbox (SCT), a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-of-the-art MM templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series. SCT is tailored towards standardization and automation of the processing pipeline, versatility, modularity, and it follows guidelines of software development and distribution. Preliminary applications of SCT cover a variety of studies, from cross-sectional area measures in large databases of patients, to the precise quantification of mpMRI metrics in specific spinal pathways. We anticipate that SCT will bring together the spinal cord neuroimaging community by establishing standard templates and analysis procedures.
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