Analysis pipelines

One of the main applications of SCT is building image analysis pipelines using SCT’s Command-Line Tools. To provide examples of this, the SCT team maintains the SCT Pipeline GitHub organization, which contains analysis pipelines used in NeuroPoly-affiliated research projects. These SCT Pipeline projects demonstrate how SCT’s command-line tools can be successfully applied to real-world MRI imaging data, and cover areas such as:

• Metric analysis (DTI, MSDKI) of pediatric (neonatal) spinal cord diffusion MRI data

• Registration and metric extraction for stroke patients

• Computation of normative qMRI metrics in specific spinal pathways

Feel free to use, share and contribute on this organization!