198 lines
5.7 KiB
ReStructuredText
198 lines
5.7 KiB
ReStructuredText
.. include:: links.inc
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Installing ``junifer``
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======================
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Depending on your use-case, ``junifer`` can be installed differently:
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* Install the :ref:`latest stable release <install_latest_release>`. This is the most suitable approach
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for end users.
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* Install from :ref:`latest development release <install_development_git>`. This is the most suitable approach
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for developers.
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Either way, we strongly recommend using
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`virtual environments <https://realpython.com/python-virtual-environments-a-primer>`_.
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.. _install_latest_release:
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Using a package manager
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-----------------------
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Use ``pip`` to install ``junifer`` from `PyPI <https://pypi.org>`_, like so:
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.. code-block:: bash
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pip install junifer
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You can also install via ``conda``, like so:
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.. code-block:: bash
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conda install -c conda-forge junifer
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.. attention::
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Installation on macOS and Windows might fail via ``conda`` due to ``datalad``.
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In that case, please refer to
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`Datalad installation instructions
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<http://handbook.datalad.org/en/latest/intro/installation.html>`_ for solutions.
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In case the problem persists, please install it via ``pip`` as mentioned earlier.
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.. _install_development_git:
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From the source
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---------------
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Follow the `detailed contribution guidelines <contribution.rst>`_.
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.. _installation_ext:
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Installing external dependencies
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================================
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Some preprocessors and markers will require optional external dependencies to
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be installed. In this section you will find a list of all external dependencies
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that are required for specific markers.
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.. important::
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The Docker container wrappers add the commands required by ``junifer``. Using
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these commands have some limitations, mostly related to handling files and
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paths. ``junifer`` knows about this and uses these commands in the proper way.
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Keep this in mind if you try to use the Docker wrappers outside of
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``junifer``. These caveats and limitations are not documented.
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AFNI
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----
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To install AFNI, you can always follow the `AFNI official instructions
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<https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html>`_.
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Additionally, you can also follow the following steps to install and configure
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the AFNI Docker container in your local system.
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1. Install Docker. You can follow the
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`Docker official instructions <https://docs.docker.com/get-docker/>`_.
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2. Pull the AFNI Docker image from
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`Docker Hub AFNI <https://hub.docker.com/r/afni/afni>`_:
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.. code-block:: bash
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docker pull afni/afni_make_build
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3. Add the Junifer AFNI scripts to your PATH environment variable. Run the
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following command:
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.. code-block:: bash
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junifer setup afni-docker
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Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
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Or, alternatively, you can execute this command which will update the
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``~/.bashrc`` for you:
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.. code-block:: bash
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junifer setup afni-docker | grep "PATH=" | xargs | >> ~/.bashrc
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FSL
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---
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To install FSL, you can always follow the `FSL official instructions
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<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation>`_.
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Additionally, you can also follow the following steps to install and configure
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the FSL Docker container in your local system.
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1. Install Docker. You can follow the
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`Docker official instructions <https://docs.docker.com/get-docker/>`_.
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2. Pull the FSL Docker image from
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`Docker Hub FSL <https://hub.docker.com/r/brainlife/fsl>`_:
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.. code-block:: bash
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docker pull brainlife/fsl
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3. Add the Junifer FSL scripts to your PATH environment variable. Run the
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following command:
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.. code-block:: bash
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junifer setup fsl-docker
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Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
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Or, alternatively, you can execute this command which will update the
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``~/.bashrc`` for you:
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.. code-block:: bash
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junifer setup fsl-docker | grep "PATH=" | xargs | >> ~/.bashrc
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ANTs
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----
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To install ANTs, you can always follow the `ANTs official instructions
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<https://github.com/ANTsX/ANTs>`_. Additionally, you can also follow the
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following steps to install and configure the ANTs Docker container in your
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local system.
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1. Install Docker. You can follow the
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`Docker official instructions <https://docs.docker.com/get-docker/>`_.
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2. Pull the ANTs Docker image from
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`Docker Hub ANTs <https://hub.docker.com/r/antsx/ants>`_:
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.. code-block:: bash
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docker pull antsx/ants
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3. Add the Junifer ANTs scripts to your PATH environment variable. Run the
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following command:
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.. code-block:: bash
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junifer setup ants-docker
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Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
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Or, alternatively, you can execute this command which will update the
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``~/.bashrc`` for you:
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.. code-block:: bash
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junifer setup ants-docker | grep "PATH=" | xargs | >> ~/.bashrc
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FreeSurfer
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----------
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To install FreeSurfer, you can always follow the `FreeSurfer official instructions
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<https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall>`_. Additionally, you can
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also follow the following steps to install and configure the FreeSurfer Docker container
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in your local system.
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1. Install Docker. You can follow the
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`Docker official instructions <https://docs.docker.com/get-docker/>`_.
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2. Pull the FreeSurfer Docker image from
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`Docker Hub FreeSurfer <https://hub.docker.com/r/freesurfer/freesurfer>`_:
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.. code-block:: bash
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docker pull freesurfer/freesurfer
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3. Add the Junifer FreeSurfer scripts to your PATH environment variable. Run the
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following command:
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.. code-block:: bash
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junifer setup freesurfer-docker
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Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
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Or, alternatively, you can execute this command which will update the
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``~/.bashrc`` for you:
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.. code-block:: bash
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junifer setup freesurfer-docker | grep "PATH=" | xargs | >> ~/.bashrc
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