Welcome to the scilpy documentation!
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scilpy is a comprehensive library that provides tools and scripts for processing, analyzing, and visualizing diffusion MRI and tractography data.
It supports advanced features such as tensor- and multi-tensor modeling, streamline registration/transformations, bundle analysis, and more.
Use scilpy to build custom diffusion pipelines or apply ready-to-use scripts.
The documentation is organized into the following sections: 

1. **Getting started & installation** — how to install, set up environments, and run a basic example
2. **Modules & API reference** — detailed descriptions of classes functions and modules
3. **Scripts & workflows** — ready scripts for common tasks

.. toctree::
   :maxdepth: 1
   :caption: Getting started

   documentation/getting_started

.. toctree::
   :maxdepth: 1
   :caption: Documentation & Tutorials

   documentation/volumes_manip/index
   documentation/reconstruction/index
   documentation/tracking/index
   documentation/tractogram_manipulation/index
   documentation/bundle_analysis/index
   documentation/connectivity/index
   documentation/start_to_finish_pipelines/index
   documentation/visualization/index
   documentation/utils/index
   documentation/scilpy_paper_index

.. toctree::
   :maxdepth: 1
   :caption: Modules and API reference

   modules/scilpy
   scripts/modules