.. _index.rst:

==============================================
dMRI Analysis
==============================================
| Contributors: Yukai Zou, Ikbeom Jang
| Maintainers: Yukai Zou

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.. warning::

    Numerous sequences and parameters exist for diffusion MRI (dMRI) data. As a result, people often end up using different software and everyone has different preprocessing pipelines. The processing steps also vary depending on how your data were acquired.

.. note::

    Under construction

This instruction focuses on the preprocessing and anlysis of diffusion tensor imaging (DTI) processing using FSL libraries. 

Here are some free educational materials that can help understand DTI:

- Book: https://www.sciencedirect.com/book/9780123964601/diffusion-mri
- http://www.diffusion-imaging.com/2013/01/relation-between-neural-microstructure.html
- http://www.diffusion-imaging.com/2014/04/from-diffusion-weighted-images-to.html
- http://www.diffusion-imaging.com/2015/10/what-is-diffusion-tensor.html
- http://clinical-mri.com/wp-content/uploads/software_hardware_updates/Graessner.pdf
- `FSL course on YouTube <https://www.youtube.com/watch?v=3ExL6J4BIeo&list=PLvgasosJnUVl_bt8VbERUyCLU93OG31h_>`_
- `DIPY 2021 workshop <https://www.youtube.com/watch?v=1aHs21YAMWA&list=PLRZ9VSqV-6soOC0rUEAOV-QiSa_Qxk8JM>`_
- `MRtrix3 B.A.T.M.A.N. on Open Science Framework <https://osf.io/fkyht/>`_
- `ITK <https://itk.org/>`_


.. toctree::
    :maxdepth: 1
    :caption: Sections

    intro
    preprocess
    analysis