.. _tutorials:

Tutorials and Courses
#####################

.. note::

   The following tutorials make use of :ref:`Quality Control (QC) <qc>` reports for inspecting processed image data. Optionally, we also recommend trying out :ref:`fsleyes-instructions` to visualize the data from these tutorials, too.

Tutorial pages
**************

We provide the following hands-on tutorials for SCT's command-line tools.

#. :doc:`Segmentation <tutorials/segmentation>`
#. :doc:`Registration to template <tutorials/registration-to-template>`

   * :doc:`tutorials/registration-to-template/vertebral-labeling`
   * :doc:`tutorials/registration-to-template/template-registration`
   * :doc:`tutorials/registration-to-template/shape-metric-computation`
   * :doc:`tutorials/registration-to-template/registering-additional-contrasts`
   * :doc:`tutorials/registration-to-template/mtr-computation`

#. :doc:`Gray matter segmentation <tutorials/gray-matter-segmentation>`

   * :doc:`tutorials/gray-matter-segmentation/gm-wm-segmentation`
   * :doc:`tutorials/gray-matter-segmentation/gm-wm-metric-computation`
   * :doc:`tutorials/gray-matter-segmentation/improving-registration-with-gm-seg`

#. :doc:`Atlas-based analysis <tutorials/atlas-based-analysis>`
#. :doc:`Diffusion-weighted MRI (Motion correction, DTI computation) <tutorials/diffusion-weighted-mri>`
#. :doc:`Other features <tutorials/other-features>`

   * :doc:`Functional MRI (Motion correction, Spinal level labeling) <tutorials/other-features/processing-fmri-data>`
   * :doc:`Spinal cord smoothing <tutorials/other-features/spinalcord-smoothing>`
   * :doc:`Visualizing misaligned cords <tutorials/other-features/visualizing-misaligned-cords>`

#. :doc:`Analysis pipelines with SCT <tutorials/analysis-pipelines-with-sct>`

.. Note: The TOC below is hidden because neither ":maxdepth: 2" nor ":maxdepth: 1" looks correct. Instead, we manually
         create our own table of contents using lists, and this will produce a good-looking hybrid of both options.

.. toctree::
   :hidden:
   :maxdepth: 2

   Segmentation <tutorials/segmentation>
   tutorials/registration-to-template
   tutorials/gray-matter-segmentation
   tutorials/atlas-based-analysis
   tutorials/diffusion-weighted-mri
   tutorials/other-features
   Analysis pipelines with SCT <tutorials/analysis-pipelines-with-sct>

SCT Course
**********

We also organize a **free** in-person SCT course each year after the ISMRM conference. The course provides a guided walkthrough of SCT, with developers and researchers on-hand to provide support and to answer any questions you may have. If you’d like to be added to the mailing list for course announcements, please visit `this link <https://docs.google.com/forms/d/e/1FAIpQLSdvsXwLRj07bx85O2wPM9ut1sC-20dFKdTVe-OckyvkfncV3Q/viewform>`_.

The past courses handouts are listed below:

-  `SCT course (v4.2.1), London, 2020-01-21`_ \| `Video recording`_
-  `SCT course (v4.0.0), Beijing, 2019-08-02`_ \| `Slides with Chinese translation`_
-  `SCT course (v4.0.0_beta.4), London, 2019-01-22`_
-  `SCT course (v3.2.2), Paris, 2018-06-12`_
-  `SCT course (v3.0.3), Honolulu, 2017-04-28`_
-  `SCT course (v3.0_beta14), Geneva, 2016-06-28`_
-  `SCT course (v3.0_beta9), Singapore, 2016-05-13`_
-  `SCT course (v3.0_beta1), Montreal, 2016-04-19`_
-  `SCT Hands-on Workshop (v2.0.4), Toronto, 2015-06-15`_

.. _SCT course (v4.2.1), London, 2020-01-21: https://drive.google.com/file/d/1TZireJ6yhV8q7PbKKXyXg7Heov9-YJMu/view?usp=sharing
.. _Video recording: https://www.youtube.com/watch?v=whbtjYNtHko&feature=youtu.be
.. _SCT course (v4.0.0), Beijing, 2019-08-02: https://osf.io/arfv7/
.. _Slides with Chinese translation: https://osf.io/hnmr2/
.. _SCT course (v4.0.0_beta.4), London, 2019-01-22: https://osf.io/gvs6f/
.. _SCT course (v3.2.2), Paris, 2018-06-12: https://osf.io/386h7/
.. _SCT course (v3.0.3), Honolulu, 2017-04-28: https://osf.io/fvnjq/
.. _SCT course (v3.0_beta14), Geneva, 2016-06-28: https://drive.google.com/file/d/0Bx3A13n3Q_EAOXktWmNVNGRhdUk/view?usp=sharing
.. _SCT course (v3.0_beta9), Singapore, 2016-05-13: https://drive.google.com/file/d/0Bx3A13n3Q_EAa3NQYjBOWjhjZm8/view?usp=sharing
.. _SCT course (v3.0_beta1), Montreal, 2016-04-19: https://drive.google.com/file/d/0Bx3A13n3Q_EAenltM2ZvZUNEdjQ/view?usp=sharing
.. _SCT Hands-on Workshop (v2.0.4), Toronto, 2015-06-15: https://www.dropbox.com/s/f9887yrbkcfujn9/sct_handsOn_20150605.pdf?dl=0


Video tutorials
***************

SCT also has a `YouTube channel`_ which contains additional tutorials.

.. _Youtube channel: https://www.youtube.com/playlist?list=PLJ5-Fnq9XpaVgCZfY-GOGJaT0fmZN4vji