Metadata-Version: 2.4
Name: heudiconv
Version: 1.5.1
Summary: Heuristic DICOM Converter
Author: HeuDiConv team and contributors
License-Expression: Apache-2.0
Project-URL: Homepage, https://github.com/nipy/heudiconv
Project-URL: Documentation, https://heudiconv.readthedocs.io
Project-URL: Source Code, https://github.com/nipy/heudiconv
Project-URL: Bug Tracker, https://github.com/nipy/heudiconv/issues
Project-URL: Changelog, https://github.com/nipy/heudiconv/blob/master/CHANGELOG.md
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering
Classifier: Typing :: Typed
Requires-Python: >=3.9
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: dcmstack>=0.8
Requires-Dist: etelemetry
Requires-Dist: filelock>=3.0.12
Requires-Dist: nibabel>=5.3.1
Requires-Dist: nipype>=1.2.3
Requires-Dist: pydicom>=1.0.0
Provides-Extra: tests
Requires-Dist: pytest; extra == "tests"
Requires-Dist: tinydb; extra == "tests"
Requires-Dist: inotify; extra == "tests"
Provides-Extra: extras
Requires-Dist: duecredit; extra == "extras"
Provides-Extra: datalad
Requires-Dist: datalad>=0.13.0; extra == "datalad"
Provides-Extra: all
Requires-Dist: heudiconv[datalad,extras,tests]; extra == "all"
Dynamic: description
Dynamic: description-content-type
Dynamic: license-file

=============
**HeuDiConv**
=============

`a heuristic-centric DICOM converter`

.. image:: https://joss.theoj.org/papers/10.21105/joss.05839/status.svg
   :target: https://doi.org/10.21105/joss.05839
   :alt: JOSS Paper

.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:latest-brightgreen.svg?logo=docker&style=flat
  :target: https://hub.docker.com/r/nipy/heudiconv/tags/
  :alt: Our Docker image

.. image:: https://github.com/nipy/heudiconv/actions/workflows/test.yml/badge.svg?event=push
  :target: https://github.com/nipy/heudiconv/actions/workflows/test.yml
  :alt: GitHub Actions (test)

.. image:: https://codecov.io/gh/nipy/heudiconv/branch/master/graph/badge.svg
  :target: https://codecov.io/gh/nipy/heudiconv
  :alt: CodeCoverage

.. image:: https://readthedocs.org/projects/heudiconv/badge/?version=latest
  :target: http://heudiconv.readthedocs.io/en/latest/?badge=latest
  :alt: Readthedocs

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1012598.svg
  :target: https://doi.org/10.5281/zenodo.1012598
  :alt: Zenodo (latest)

.. image:: https://repology.org/badge/version-for-repo/debian_unstable/heudiconv.svg?header=Debian%20Unstable
   :target: https://repology.org/project/heudiconv/versions
   :alt: Debian Unstable

.. image:: https://repology.org/badge/version-for-repo/gentoo_ovl_science/python:heudiconv.svg?header=Gentoo%20%28%3A%3Ascience%29
   :target: https://repology.org/project/python:heudiconv/versions
   :alt: Gentoo (::science)

.. image:: https://repology.org/badge/version-for-repo/pypi/python:heudiconv.svg?header=PyPI
   :target: https://repology.org/project/python:heudiconv/versions
   :alt: PyPI

.. image:: https://img.shields.io/badge/RRID-SCR__017427-blue
   :target: https://identifiers.org/RRID:SCR_017427
   :alt: RRID

About
-----

``heudiconv`` is a flexible DICOM converter for organizing brain imaging data
into structured directory layouts.

- It allows flexible directory layouts and naming schemes through customizable heuristics implementations.
- It only converts the necessary DICOMs and ignores everything else in a directory.
- You can keep links to DICOM files in the participant layout.
- Using `dcm2niix <https://github.com/rordenlab/dcm2niix/>`_ under the hood, it's fast.
- It can track the provenance of the conversion from DICOM to NIfTI in W3C PROV format.
- It provides assistance in converting to `BIDS <http://bids.neuroimaging.io/>`_.
- It integrates with `DataLad <https://www.datalad.org/>`_ to place converted and original data under git/git-annex
  version control while automatically annotating files with sensitive information (e.g., non-defaced anatomicals, etc).

Heudiconv can be inserted into your workflow to provide automatic conversion as part of a data acquisition pipeline, as seen in the figure below:

.. image:: https://raw.githubusercontent.com/nipy/heudiconv/master/figs/environment.png

Installation
------------

See our `installation page <https://heudiconv.readthedocs.io/en/latest/installation.html>`_
on heudiconv.readthedocs.io .

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:: https://raw.githubusercontent.com/nipy/heudiconv/master/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.

In most use-cases of retrospective study data conversion, you would need to create your custom heuristic following the examples and the `"Heuristic" section <https://heudiconv.readthedocs.io/en/latest/heuristics.html>`_ in the documentation.
**Note** that `ReproIn heuristic <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py>`_ is
generic and powerful enough to be adopted virtually for *any* study: For prospective studies, you would just need
to name your sequences following the `ReproIn convention <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py#L26>`_, and for
retrospective conversions, you often would be able to create a new versatile heuristic by simply providing
remappings into ReproIn as shown in `this issue (documentation is coming) <https://github.com/ReproNim/reproin/issues/18#issuecomment-834598084>`_.

Having decided on a heuristic, you could use the command line::

    heudiconv -f HEURISTIC-FILE-OR-NAME -o OUTPUT-PATH --files INPUT-PATHs

with various additional options (see ``heudiconv --help`` or
`"CLI Reference" in documentation <https://heudiconv.readthedocs.io/en/latest/commandline.html>`__) to tune its behavior to
convert your data.

For detailed examples and guides, please check out `ReproIn conversion invocation examples <https://github.com/ReproNim/reproin/#conversion>`_
and the `user tutorials <https://heudiconv.readthedocs.io/en/latest/tutorials.html>`_ in the documentation.


How to cite
-----------

Please use `Zenodo record <https://doi.org/10.5281/zenodo.1012598>`_ for
your specific version of HeuDiConv.  We also support gathering
all relevant citations via `DueCredit <http://duecredit.org>`_.


How to contribute
-----------------

For a detailed into, see our `contributing guide <https://github.com/nipy/heudiconv/blob/master/CONTRIBUTING.rst>`_.

Our releases are packaged using Intuit auto, with the corresponding workflow including
Docker image preparation being found in ``.github/workflows/release.yml``.


3-rd party heuristics
---------------------

- https://github.com/courtois-neuromod/ds_prep/blob/main/mri/convert/heuristics_unf.py


Support
-------

All bugs, concerns and enhancement requests for this software can be submitted here:
https://github.com/nipy/heudiconv/issues.

If you have a problem or would like to ask a question about how to use ``heudiconv``,
please submit a question to `NeuroStars.org <http://neurostars.org/tags/heudiconv>`_ with a ``heudiconv`` tag.
NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.

All previous ``heudiconv`` questions are available here:
http://neurostars.org/tags/heudiconv/ .
