Analysis pipelines
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One of the main applications of SCT is building image analysis pipelines using SCT's :ref:`command-line-tools`. To provide examples of this, the SCT team maintains the `SCT Pipeline <https://github.com/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 <https://github.com/sct-pipeline/pediatric-genova>`_
- `Registration and metric extraction for stroke patients <https://github.com/sct-pipeline/levin-stroke>`_
- `Computation of normative qMRI metrics in specific spinal pathways <https://github.com/sct-pipeline/normative-metrics>`_

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