@@ -6,73 +6,39 @@ dmriprep
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.. image :: https://img.shields.io/pypi/v/dmriprep.svg
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:target: https://pypi.python.org/pypi/dmriprep
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- .. image :: https://img.shields.io/travis/akeshavan/dmriprep.svg
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- :target: https://travis-ci.org/akeshavan/dmriprep
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.. image :: https://readthedocs.org/projects/dmriprep/badge/?version=latest
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:target: https://dmriprep.readthedocs.io/en/latest/?badge=latest
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:alt: Documentation Status
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- Preprocessing of neuroimaging data in preparation for AFQ analysis
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-
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-
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- * Free software: BSD license
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- * Documentation: https://dmriprep.readthedocs.io.
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-
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-
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- Features
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- --------
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-
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- * TODO
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-
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-
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- Contributing
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- ------------
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-
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- We love contributions! dmriprep is open source, built on open source,
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- and we'd love to have you hang out in our community.
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-
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- We have developed some `guidelines `_ for contributing to dmriprep.
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-
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- **Imposter syndrome disclaimer **: We want your help. No, really.
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-
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- There may be a little voice inside your head that is telling you that
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- you're not ready to be an open source contributor; that your skills
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- aren't nearly good enough to contribute. What could you possibly offer a
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- project like this one?
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-
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- We assure you - the little voice in your head is wrong. If you can
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- write code at all, you can contribute code to open source. Contributing
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- to open source projects is a fantastic way to advance one's coding
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- skills. Writing perfect code isn't the measure of a good developer (that
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- would disqualify all of us!); it's trying to create something, making
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- mistakes, and learning from those mistakes. That's how we all improve,
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- and we are happy to help others learn.
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-
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- Being an open source contributor doesn't just mean writing code, either.
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- You can help out by writing documentation, tests, or even giving
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- feedback about the project (and yes - that includes giving feedback
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- about the contribution process). Some of these contributions may be the
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- most valuable to the project as a whole, because you're coming to the
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- project with fresh eyes, so you can see the errors and assumptions that
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- seasoned contributors have glossed over.
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-
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-
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- Credits
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- -------
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-
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- This package was created with Cookiecutter _ and the `audreyr/cookiecutter-pypackage `_ project template.
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-
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- The imposter syndrome disclaimer was originally written by `Adrienne
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- Lowe `_ for a `PyCon talk `_, and was adapted based on its use in the
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- README file for the `MetPy project `_.
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-
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- .. _Cookiecutter : https://github.com/audreyr/cookiecutter
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- .. _`audreyr/cookiecutter-pypackage` : https://github.com/audreyr/cookiecutter-pypackage
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- .. _`Adrienne Lowe` : https://github.com/adriennefriend
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- .. _`Pycom talk` : https://www.youtube.com/watch?v=6Uj746j9Heo
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- .. _`MetPy project` : https://github.com/Unidata/MetPy
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- .. _`guidelines` : CONTRIBUTING.rst
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+ Preprocessing of diffusion MRI (dMRI) involves numerous steps to clean and standardize
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+ the data before fitting a particular model.
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+ Generally, researchers create ad hoc preprocessing workflows for each dataset,
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+ building upon a large inventory of available tools.
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+ The complexity of these workflows has snowballed with rapid advances in
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+ acquisition and processing.
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+ dMRIPrep is an analysis-agnostic tool that addresses the challenge of robust and
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+ reproducible preprocessing for whole-brain dMRI data.
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+ dMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of
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+ virtually any dataset, ensuring high-quality preprocessing without manual intervention.
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+ dMRIPrep equips neuroscientists with an easy-to-use and transparent preprocessing
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+ workflow, which can help ensure the validity of inference and the interpretability
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+ of results.
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+
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+ The workflow is based on `Nipype <https://nipype.readthedocs.io >`_ and encompases a large
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+ set of tools from well-known neuroimaging packages, including
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+ `FSL <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ >`_,
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+ `ANTs <https://stnava.github.io/ANTs/ >`_,
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+ `FreeSurfer <https://surfer.nmr.mgh.harvard.edu/ >`_,
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+ `AFNI <https://afni.nimh.nih.gov/ >`_,
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+ and `Nilearn <https://nilearn.github.io/ >`_.
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+ This pipeline was designed to provide the best software implementation for each state of
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+ preprocessing, and will be updated as newer and better neuroimaging software becomes
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+ available.
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+
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+ dMRIPrep performs basic preprocessing steps (coregistration, normalization, unwarping,
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+ segmentation, skullstripping etc.) providing outputs that can be
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+ easily submitted to a variety of tractography algorithms.
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+
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+ [Documentation `dmriprep.org <https://dmriprep.readthedocs.io >`_]
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+ [Support `neurostars.org <https://neurostars.org/tags/fmriprep >`_]
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