Beginner DWI tutorial
=====================
.. TIP::
Some proficiency with the Unix command-line is required to make the best use
of this software. There are many resources online to help you get
started if you are not already familiar with it. We also recommend our own
`Introduction to the Unix command-line
`__, which was written with a
particular focus on the types of use that are common when using *MRtrix3*.
.. WARNING::
This tutorial is not intended to show the optimal or even recommended way of
processing. It is merely a simplified example, intended to familiarise the
user with the typical command line interface of certain basic processing
steps.
This tutorial will hopefully provide enough information for a novice
user to get from the raw DW image data to performing some streamlines
tractography. It may also be useful for experienced MRtrix users in
terms of identifying some of the new command names.
For all *MRtrix3* scripts and commands, additional information on the
command usage and available command-line options can be found by
invoking the command with the ``-help`` option. Note that this tutorial
includes commands and scripts for which there are relevant journal
articles for citation; these are listed on the help pages also.
DWI geometric distortion correction
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If the user has access to reversed phase-encode spin-echo image data,
this can be used to correct the susceptibility-induced geometric
distortions present in the diffusion images, as well as any eddy
current-induced distortions and inter-volume subject motion. Procedures
for this correct are not yet implemented in *MRtrix3*, though we do provide
a script for interfacing with the relevant FSL tools:
``dwifslpreproc