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Adding workflow figure
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TheChymera committed Jan 12, 2024
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Expand Up @@ -66,6 +66,11 @@ HOWTO 101

In a nutshell -- ``heudiconv`` is given a file tree of DICOMs, and it produces a restructured file tree of NifTI files (conversion handled by `dcm2niix`_) with accompanying metadata files.
The input and output structure is as flexible as your data, which is accomplished by using a Python file called a ``heuristic`` that knows how to read your input structure and decides how to name the resultant files.
You can run your conversion automatically (which will produce a ``.heudiconv`` directory storing the used parameters), or generate the default parameters, edit them to customize file naming, and continue conversion via an additional invocation of `heudiconv`:

.. image:: figs/workflow.png


``heudiconv`` comes with `existing heuristics <https://github.com/nipy/heudiconv/tree/master/heudiconv/heuristics>`_ which can be used as is, or as examples.
For instance, the Heuristic `convertall <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/convertall.py>`_ extracts standard metadata from all matching DICOMs.
``heudiconv`` creates mapping files, ``<something>.edit.text`` which lets researchers simply establish their own conversion mapping.
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