<commit_before>Motivation for ``afdconnectivity``
==================================


Due to the interest in the :ref:`afdconnectivity` command, I thought I'd
explain the reasoning behind the approach, the rationale behind the
improvements made in commit 40ccdb62, and the argument for why we
recommend the use of :ref:`sift` as an alternative if possible.

The ``afdconnectivity`` command was originally written as a 'hack' for a
colleague who wanted to obtain quantitative measures of 'connectivity'
in the absence of EPI distortion correction. Without EPI distortion
correction :ref:`act` cannot
be applied, and consequently streamlines may terminate within white
matter. Streamline count (as a measure of connectivity) between two grey
matter regions will therefore not include those streamlines that
terminate in white matter (and therefore the estimated connectivity may
not be accurate).

The afdconnectivity command attempts to get around this issue by
estimating a measure of 'connectivity' as follows:

-  The integral of a discrete lobe of an FOD
   (:ref:`fixel <fixels_dixels>`) is proportional to the volume of
   the MR-visible tissue (intra-cellular at high *b*-value) aligned in
   that direction.

-  By taking a set of streamlines corresponding to a pathway of
   interest, and summing the integrals of all FOD lobes traversed by the
   bundle, you obtain an estimate of the total fibre volume of the
   pathway of interest.<commit_msg>Docs: afdconnectivity: Link to preprint<commit_after>Motivation for ``afdconnectivity``
==================================

.. NOTE::

    A `preprint <https://osf.io/c67kn/>`_ has now been uploaded, which
    expands on the concepts within this page with figures and greater detail,
    and includes explanation of the newer SIFT2 method available in command
    :ref:`tcksift2`. Readers may find it more informative and up-to-date than
    the content of this documentation page.

Due to the interest in the :ref:`afdconnectivity` command, I thought I'd
explain the reasoning behind the approach, the rationale behind the
improvements made in commit 
`40ccdb62 <https://github.com/MRtrix3/mrtrix3/commit/40ccdb6290ccac81252747d5be71a77af56e8dc6>`_, 
and the argument for why we recommend the use of :ref:`sift` as an
alternative if possible.

The ``afdconnectivity`` command was originally written as a 'hack' for a
colleague who wanted to obtain quantitative measures of 'connectivity'
in the absence of EPI distortion correction. Without EPI distortion
correction :ref:`act` cannot
be applied, and consequently streamlines may terminate within white
matter. Streamline count (as a measure of connectivity) between two grey
matter regions will therefore not include those streamlines that
terminate in white matter (and therefore the estimated connectivity may
not be accurate).

The afdconnectivity command attempts to get around this issue by
estimating a measure of 'connectivity' as follows:

-  The integral of a discrete lobe of an FOD
   (:ref:`fixel <fixels_dixels>`) is proportional to the volume of
   the MR-visible tissue (intra-cellular at high *b*-value) aligned in
   that direction.

-  By taking a set of streamlines corresponding to a pathway of
   interest, and summing the integrals of all FOD lobes traversed by the
   bundle, you obtain an estimate of the total fibre volume of the
   pathway of interest.
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