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Merge pull request #741 from yarikoptic/bf-doc
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Adjust wording on heuristics page -- do not claim creating some skeleton
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yarikoptic authored Feb 24, 2024
2 parents e059ad7 + fd1f838 commit 7b98ae7
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21 changes: 12 additions & 9 deletions docs/heuristics.rst
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Expand Up @@ -3,22 +3,25 @@ Heuristics File
===============

The heuristic file controls how information about the DICOMs is used to convert
to a file system layout (e.g., BIDS). ``heudiconv`` includes some built-in
heuristics, including `ReproIn <https://github.com/ReproNim/reproin/blob/master/README.md>`_
(which is great to adopt if you will be starting your data collection!).

However, there is a large variety of data out there, and not all DICOMs will be
covered by the existing heuristics. This section will outline what makes up a
heuristic file, and some useful functions available when making one.
to a file system layout (e.g., BIDS).


Provided Heuristics
-------------------

Running ``heudiconv`` without a heuristic file results in the generation of a skeleton for the user to customize to their needs.
``heudiconv`` provides over 10 pre-created heuristics, which can be seen `here <https://github.com/nipy/heudiconv/tree/master/heudiconv/heuristics>`_ .

``heudiconv`` also provides more than 10 additional heuristics, which can be seen `here <https://github.com/nipy/heudiconv/tree/master/heudiconv/heuristics>`_
These heuristic files are documented in their code comments.
Some of them, like `convertall <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/convertall.py>`_ or `ReproIn <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py>`__ could be immediately reused and represent two ends of the spectrum in heuristics:

- ``convertall`` is very simple and does not automate anything -- it is for a user to modify filenames in the prepared conversion table, and then rerun with ``-c dcm2niix``.
- ``reproin`` can be used fully automated, if original sequences were named according to its ReproIn convention.

Discover more on their user in the :ref:`Tutorials` section.

However, there is a large variety of data out there, and not all DICOMs
will be covered by the existing heuristics. This section will outline what
makes up a heuristic file, and some useful functions available when making one.

Components
==========
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5 changes: 3 additions & 2 deletions docs/tutorials.rst
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.. _Tutorials:

==================
=========
Tutorials
==================
=========

.. toctree::

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