.. _gui:

3D Slicer GUI
-------------

`3D Slicer <https://www.slicer.org/>`_ is an open-source software platform for
medical image informatics, image processing,
and three-dimensional visualization.

TorchIO provides a 3D Slicer extension for quick experimentation and
visualization of the package features without any coding.

The TorchIO extension can be easily installed using the
`Extensions Manager <https://slicer.readthedocs.io/en/latest/user_guide/extensions_manager.html>`_.

The code and installation instructions are available on
`GitHub <https://github.com/fepegar/SlicerTorchIO>`_.

.. note:: The Preview version (built nightly) is recommended. You can download
    and install Slicer from `their download website <https://download.slicer.org/>`_
    or, if you are on macOS, using `Homebrew <https://docs.brew.sh/>`_::

        brew tap homebrew/cask-versions && brew cask install slicer-preview


TorchIO Transforms
^^^^^^^^^^^^^^^^^^

This module can be used to quickly visualize the effect of each transform
parameter.
That way, users can have an intuitive feeling of what the output
of a transform looks like without any coding at all.

.. image:: https://raw.githubusercontent.com/fepegar/SlicerTorchIO/master/Screenshots/TorchIO.png
    :alt: TorchIO Transforms module for 3D Slicer


Usage example
"""""""""""""

Go to the ``Sample Data`` module to get an image we can use:

.. image:: https://raw.githubusercontent.com/fepegar/SlicerTorchIO/master/Screenshots/usage_1.png
    :alt: Go to Sample Data module


Click on an image to download, for example MRHead [#]_,
and go to the ``TorchIO Transforms`` module:

.. [#] All the data in ``Sample Data`` can be downloaded and used in the TorchIO
    Python library using the :class:`torchio.datasets.slicer.Slicer` class.

.. image:: https://raw.githubusercontent.com/fepegar/SlicerTorchIO/master/Screenshots/usage_2.png
    :alt: Download MRHead and go to TorchIO Transforms module


Select the input and output volume nodes:

.. image:: https://raw.githubusercontent.com/fepegar/SlicerTorchIO/master/Screenshots/usage_3.png
    :alt: Select volume nodes


Modify the transform parameters and click on ``Apply transform``.
Hovering the mouse over the transforms will show tooltips extracted from the
TorchIO documentation.

.. image:: https://raw.githubusercontent.com/fepegar/SlicerTorchIO/master/Screenshots/usage_4.png
    :alt: Apply transform


You can click on the ``Toggle volumes`` button to switch between input and
output volumes.