Where to get trekker?
=========================================

.. note::

   .. centered:: Citation information

   If you use trekker in your study, please cite our work. Click `here <../publications/publications.html>`__ for more information.


Stand-alone executables
-----------------------

You can download precompiled stand-alone executables from `here <https://github.com/dmritrekker/trekker/tree/master/binaries>`__ for:

- *Linux*: Tested on Debian (versions 9 and 10) and Red Hat Enterprise Linux 6.

- *Windows*: Tested on Windows 10.

- *Mac OS*: A stand-alone executable does not exist.



Source code
-----------

*Step 1*. Download the source code from `github <https://github.com/dmritrekker/trekker>`__, using:
  ::

    git clone https://github.com/dmritrekker/trekker

*Step 2*. Modify the first few lines in the build script (make sure to have cmake-3.15 or newer):
  - For Linux -> build_Linux.sh
  - For Windows -> build_Windows.bat

*Step 3*. Run the build script. This will build Trekker:
  - For Linux -> <TrekkerFolder>/build/Linux/install
  - For Windows -> <TrekkerFolder>/build/Windows/install

Under the <TrekkerFolder>/install folder, the following will be generated:
  1. :code:`trekker` executable under :code:`/bin`
  2. Static and shared libraries under :code:`/lib` with library header under :code:`/include`
  3. If specified, a python built distribution (.whl) under :code:`/python/dist`


Python package
--------------

A python package can be built from source. You can also download a built distributions (.whl) from `here <https://github.com/dmritrekker/trekker/tree/master/binaries>`__.

To install the python package use:

::

    pip install Trekker-<VERSION>.whl

Test your installation
======================

You can use the demo scripts in `here <https://github.com/dmritrekker/trekker/tree/master/demo>`__ for testing your installation.



Extensions
==========

- **Matlab**: Trekker formatted .vtk files can be read in Matlab using the following function, :code:`extensions/matlab/readTrekkerOutput.m`.

- **LONI pipeline**: A LONI pipeline module and workflow examples for Trekker can be found under: :code:`extensions/LONI_Pipeline/`.

- **trekker_mergeTracksWithPrefix**: This tool can be used to merge Trekker formatted (.vtk) tractograms inside a folder that start with given filename prefix.

- **trekker_addColor**: This tool can be used to add direction coded color information for each segment in a Trekker formatted (.vtk) tractogram.