Modules
=======

A pipeline is a list of modules, and a protocol gives the value of each of their options. These pages are generated from the module definitions (``<MODULE>.yml`` next to the code of each module), so they describe the modules of this version.

A module writes its results into its own folder of the output directory, and the pipeline passes the image from one module to the next. ``make-protocols`` writes a protocol with the defaults listed here, which can then be edited.

.. toctree::
   :maxdepth: 2

   dmriprep
   dmrifiberprofile