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‎CHANGES.rst

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0.1.0 (2018-09-06)
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==================
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* First release on GitHub.
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‎CONTRIBUTING.rst

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Contributing
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============
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Contributions are welcome, and they are greatly appreciated! Every little bit
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helps, and credit will always be given.
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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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**Imposter syndrome disclaimer**: We want your help. No, really.
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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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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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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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Installing a development version of dmriprep
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--------------------------------------------
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$ git push --tags
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Travis will then deploy to PyPI if tests pass.
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The imposter syndrome disclaimer was originally written by
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`Adrienne Lowe <https://github.com/adriennefriend>`_ for a `PyCon talk <https://www.youtube.com/watch?v=6Uj746j9Heo>`_, and was
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adapted based on its use in the README file for the `MetPy project <https://github.com/Unidata/MetPy>`_.

‎HISTORY.rst

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‎README.rst

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You should have raw data organized in the BIDS format. Also, you should have run Freesurfer and the results should be in a derivatives/ folder:
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```
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bids
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├── derivatives
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│   └── sub-01
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│   └── freesurfer
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└── sub-01
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├── dwi
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│   ├── sub-01_ses-01_dwi.bval
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│   ├── sub-01_ses-01_dwi.bvec
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│   ├── sub-01_ses-01_dwi.json
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│   └── sub-01_ses-01_dwi.nii.gz
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└── fmap
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├── sub-01_ses-01_acq-dwi_dir-AP_epi.json
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├── sub-01_ses-01_acq-dwi_dir-AP_epi.nii.gz
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├── sub-01_ses-01_acq-dwi_dir-PA_epi.json
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└── sub-01_ses-01_acq-dwi_dir-PA_epi.nii.gz
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```
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Quickstart
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----------
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.. code-block:: bash
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git clone https://github.com/tigrlab/dmriprep
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cd dmriprep
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python setup.py install
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dmriprep $BIDS_INPUT_DIR $OUTPUT_DIR --participant-label 01
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.. code-block:: bash
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git clone https://github.com/tigrlab/dmriprep
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cd dmriprep
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make docker
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If you don't want to log into the docker image:
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.. code-block:: bash
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docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod dmriprep /inputs /outputs
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If you want to log into the image:
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.. code-block:: bash
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docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod
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Run this inside the docker image:
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.. code-block:: bash
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dmriprep /inputs /output --participant-label 01
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.. code-block:: console
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bids
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├── derivatives
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│   └── sub-01
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│   └── freesurfer
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└── sub-01
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├── dwi
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│   ├── sub-01_ses-01_dwi.bval
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│   ├── sub-01_ses-01_dwi.bvec
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│   ├── sub-01_ses-01_dwi.json
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│   └── sub-01_ses-01_dwi.nii.gz
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└── fmap
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├── sub-01_ses-01_acq-dwi_dir-AP_epi.json
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├── sub-01_ses-01_acq-dwi_dir-AP_epi.nii.gz
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├── sub-01_ses-01_acq-dwi_dir-PA_epi.json
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└── sub-01_ses-01_acq-dwi_dir-PA_epi.nii.gz
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Features
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--------
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* TODO
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Contributing
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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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We have developed some [guidelines](CONTRIBUTING.rst) for contributing to
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dmriprep.
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**Imposter syndrome disclaimer**: We want your help. No, really.
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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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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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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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Credits
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-------
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This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [`audreyr/cookiecutter-pypackage`](https://github.com/audreyr/cookiecutter-pypackage) project template.
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The imposter syndrome disclaimer was originally written by
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[Adrienne Lowe](https://github.com/adriennefriend) for a [PyCon
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talk](https://www.youtube.com/watch?v=6Uj746j9Heo), and was
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adapted based on its use in the README file for the [MetPy
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project](https://github.com/Unidata/MetPy).
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This package was created with `Cookiecutter <https://github.com/audreyr/cookiecutter>`_ and the `audreyr/cookiecutter-pypackage <https://github.com/audreyr/cookiecutter-pypackage>`_ project template.

‎docs/changes.rst

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----------
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What's new
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----------
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.. includes:: ../CHANGES.rst

‎docs/conf.py

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#
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import os
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import sys
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from datetime import datetime
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sys.path.insert(0, os.path.abspath(".."))
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.viewcode",
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"sphinx_click.ext"
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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# General information about the project.
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project = "dmriprep"
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copyright = "2018, Anisha Keshavan"
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author = "Anisha Keshavan"
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copyright = "2018-%s, %s" % (datetime.now().year, author)
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# The version info for the project you're documenting, acts as replacement
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# for |version| and |release|, also used in various other places throughout
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = "alabaster"
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html_theme = "sphinx_rtd_theme"
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# Theme options are theme-specific and customize the look and feel of a
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# theme further. For a list of options available for each theme, see the
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master_doc,
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"dmriprep.tex",
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"dmriprep Documentation",
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"Anisha Keshavan",
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author,
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"manual",
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)
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]

‎docs/history.rst

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‎docs/index.rst

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readme
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installation
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changes
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usage
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workflows
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outputs
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contributing
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authors
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history
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Indices and tables
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==================

‎docs/installation.rst

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.. code-block:: console
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$ git clone git://github.com/tigrlab/dmriprep
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$ git clone git://github.com/josephmje/dmriprep
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Or download the `tarball`_:
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.. code-block:: console
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$ curl -OL https://github.com/tigrlab/dmriprep/tarball/master
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$ curl -OL https://github.com/josephmje/dmriprep/tarball/master
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Once you have a copy of the source, you can install it with:
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$ python setup.py install
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.. _Github repo: https://github.com/tigrlab/dmriprep
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.. _tarball: https://github.com/tigrlab/dmriprep/tarball/master
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.. _Github repo: https://github.com/josephmje/dmriprep
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.. _tarball: https://github.com/josephmje/dmriprep/tarball/master
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Docker container
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----------------
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.. code-block:: console
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$ git clone https://github.com/josephmje/dmriprep
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$ cd dmriprep
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$ make docker
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If you don't want to log into the docker image:
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.. code-block:: console
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$ docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod dmriprep /inputs /outputs
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If you want to log into the image:
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.. code-block:: console
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$ docker run -ti -v $BIDS_INPUT_DIR:/inputs -v $OUTPUT_DIR:/outputs dmriprep:prod
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Run this inside the docker image:
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.. code-block:: console
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$ dmriprep /inputs /output --participant-label 01

‎docs/links.rst

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.. _Nipype: http://nipype.readthedocs.io/en/latest/
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.. _BIDS: http://bids.neuroimaging.io
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.. _Usage: usage.html
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.. _Installation: installation.html
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.. _workflows: workflows.html
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.. _guidelines: contributing.html

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