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        <center><img src="static/images/logoNipype_tutorial.png" width=700></center>
        <p>Welcome to the Nipype Tutorial! It covers the basic concepts and most common use cases of Nipype and will teach
            you everything so that you can start creating your own workflows in no time. We recommend that you start with
            the introduction section to familiarize yourself with the tools used in this tutorial and then move on to the
            basic concepts section to learn everything you need to know for your everyday life with Nipype. The workflow
            examples section shows you a real example of how you can use Nipype to analyze an actual dataset. For a very 
            quick non-imaging introduction, you can check the Nipype Quickstart notebooks in the introduction section.
            </p><p>
            All of the notebooks used in this tutorial can be found on <a href="https://github.com/miykael/nipype_tutorial">github.com/miykael/nipype_tutorial</a>.
            But if you want to have the real experience and want to go through the computations by yourself, we highly
            recommend you to use a Docker container. More about the Docker image that can be used to run the tutorial can be found 
            <a href="https://miykael.github.io/nipype_tutorial/notebooks/introduction_docker.html">here</a>.
            This docker container gives you the opportunity to adapt the commands to your liking and discover the flexibility and real power of
            Nipype yourself.
            </p><p>
            To run the tutorial locally on your system, we will use a <a href="http://www.docker.com/">Docker</a> container. For this you
            need to install Docker and download a docker image that provides you a neuroimaging environment based on a Debian system,
            with working Python 3 software (including Nipype, dipy, matplotlib, nibabel, nipy, numpy, pandas, scipy, seaborn and more),
            FSL, ANTs and SPM12 (no license needed). We used <a href="https://github.com/kaczmarj/neurodocker">Neurodocker</a> to create this docker image.
            </p><p>
            If you do not want to run the tutorial locally, you can also use 
            <a href="https://mybinder.org/v2/gh/miykael/nipype_tutorial/master">Binder service</a>. 
            Binder automatically launches the Docker container for you and you have access to all of the notebooks. 
            Note, that Binder provides between 1G and 4G RAM memory, some notebooks from Workflow Examples might not work. 
            All notebooks from Introduction and Basic Concepts parts should work.
           </p><p>
            For everything that isn't covered in this tutorial, check out the <a href="http://nipype.readthedocs.io/en/latest/">main homepage</a>.
            And if you haven't had enough and want to learn even more about Nipype and Neuroimaging, make sure to look at
            the <a href="https://miykael.github.io/nipype-beginner-s-guide/">detailed beginner's guide</a>.
            </p>
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      <h2 class="domain-header color01"><a class="domain-title">Introduction</a></h2>
      <div class="pure-g domain-table-container color01">
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_nipype.html">Nipype</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_jupyter-notebook.html">Jupyter-Notebook</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_dataset.html">BIDS & Tutorial Dataset</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_docker.html">Docker</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_neurodocker.html">Neurodocker</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_python.html">Python</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_showcase.html">Nipype Showcase</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_quickstart.html">Nipype Quickstart</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/introduction_quickstart_non-neuroimaging.html">Nipype Quickstart (non-neuroimaging examples)</a>
      </div>
      <p>This section is meant as a general overview. It should give you a short introduction to the main topics that
          you need to understand to use Nipype and this tutorial. The section also contains a very short neuroimaging showcase, as well as quick non-imaging introduction to Nipype workflows.</p>

      <h2 class="domain-header color02"><a class="domain-title">Basic Concepts</a></h2>
      <div class="pure-g domain-table-container color02">
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_interfaces.html">Interfaces</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_nodes.html">Nodes</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_workflow.html">Workflow</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_graph_visualization.html">Graph Visualization</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_data_input.html">Data Input</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_data_input_bids.html">Data Input with BIDS</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_data_output.html">Data Output</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_plugins.html">Execution Plugins</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_function_interface.html">Function Interface</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_iteration.html">Iteration / Iterables</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_mapnodes.html">MapNodes</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_joinnodes.html">JoinNode, synchronize & itersource</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_error_and_crashes.html">Errors & Crashes</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_debug.html">Debugging Nipype Workflows</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_model_specification_fmri.html">fMRI Model Specification</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_execution_configuration.html">Execution Configuration</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/basic_import_workflows.html">Import existing Workflows</a>
      </div>
      <p>This section will introduce you to all of the key players in Nipype. Basic concepts that you need to learn to
          fully understand and appreciate Nipype. Once you understand this section, you will know all that you need to know
          to create any kind of Nipype workflow.</p>

      <h2 class="domain-header color03"><a class="domain-title">Workflow Examples</a></h2>
      <div class="pure-g domain-table-container color03">
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/example_preprocessing.html">Example 1: Preprocessing</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/example_1stlevel.html">Example 1: 1st-level Analysis</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/example_normalize.html">Example 1: Normalize Data</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/example_2ndlevel.html">Example 1: 2nd-level Analysis</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/handson_preprocessing.html">Hands-on 1: Preprocessing</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/handson_analysis.html">Hands-on 1: Analysis</a>
      </div>
      <p>In this section, you will find some practical examples and hands-on that show you how to use Nipype in a "real world" scenario.</p>

      <h2 class="domain-header color04"><a class="domain-title">Advanced Concepts</a></h2>
      <div class="pure-g domain-table-container color04">
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_create_interfaces.html">Create Interfaces</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_interfaces_caching.html">Interfaces Caching</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_nipypecli.html">Nipype Command Line Interface</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_aws.html">Amazon Web Services (AWS)</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_sphinx_ext.html">Sphinx extensions</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_spmmcr.html">SPM with MATLAB Common Runtime (MCR)</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/advanced_mipav.html">Using MIPAV, JIST, and CBS Tools</a>      </div>
      <p>This section is for more advanced users and Nipype developers.</p>

      <h2 class="domain-header color05"><a class="domain-title">Useful Resources & Links</a></h2>
      <div class="pure-g domain-table-container color05">
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/resources_installation.html">Install Nipype</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/resources_resources.html">Useful Resources & Links</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/resources_help.html">Where to find Help</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="notebooks/resources_python_cheat_sheet.html">Python Cheat Sheet</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="http://nipype.readthedocs.io/en/latest/">Nipype (main homepage)</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://miykael.github.io/nipype-beginner-s-guide/">Nipype Beginner's Guide</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://github.com/miykael/nipype_tutorial">Github of Nipype Tutorial</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://github.com/kaczmarj/neurodocker">Neurodocker</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="http://nipy.org/nibabel/">NiBabel</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="http://nilearn.github.io/">Nilearn</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://openneuro.org/">OpenNeuro</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="http://bids-apps.neuroimaging.io">BIDS Apps</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="http://fmriprep.readthedocs.io/en/latest/index.html">fmriprep</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://mriqc.readthedocs.io/en/latest/#">MRIQC</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://www.mindboggle.info/">Mindboggle</a>
        <a class="subject-link pure-u-1-4" target="_blank" href="https://timvanmourik.github.io/Porcupine/">PORcupine</a>
      </div>
      <p>This section will give you helpful links and resources so that you always know where to go to learn more.</p>

    </div>
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<h2>You want to help with this tutorial?</h2>
<p>Find the github repo of this tutorial under <a href="https://github.com/miykael/nipype_tutorial">https://github.com/miykael/nipype_tutorial</a>.
    Feel free to send a pull request or leave an <a href="https://github.com/miykael/nipype_tutorial/issues">issue</a> with your feedback or ideas.
</p>

Welcome to the Nipype Tutorial! It covers the basic concepts and most common use cases of Nipype and will teach you everything so that you can start creating your own workflows in no time. We recommend that you start with the introduction section to familiarize yourself with the tools used in this tutorial and then move on to the basic concepts section to learn everything you need to know for your everyday life with Nipype. The workflow examples section shows you a real example of how you can use Nipype to analyze an actual dataset. For a very quick non-imaging introduction, you can check the Nipype Quickstart notebooks in the introduction section.

All of the notebooks used in this tutorial can be found on github.com/miykael/nipype_tutorial. But if you want to have the real experience and want to go through the computations by yourself, we highly recommend you to use a Docker container. More about the Docker image that can be used to run the tutorial can be found here. This docker container gives you the opportunity to adapt the commands to your liking and discover the flexibility and real power of Nipype yourself.

To run the tutorial locally on your system, we will use a Docker container. For this you need to install Docker and download a docker image that provides you a neuroimaging environment based on a Debian system, with working Python 3 software (including Nipype, dipy, matplotlib, nibabel, nipy, numpy, pandas, scipy, seaborn and more), FSL, ANTs and SPM12 (no license needed). We used Neurodocker to create this docker image.

If you do not want to run the tutorial locally, you can also use Binder service. Binder automatically launches the Docker container for you and you have access to all of the notebooks. Note, that Binder provides between 1G and 4G RAM memory, some notebooks from Workflow Examples might not work. All notebooks from Introduction and Basic Concepts parts should work.

For everything that isn't covered in this tutorial, check out the main homepage. And if you haven't had enough and want to learn even more about Nipype and Neuroimaging, make sure to look at the detailed beginner's guide.

Introduction

This section is meant as a general overview. It should give you a short introduction to the main topics that you need to understand to use Nipype and this tutorial. The section also contains a very short neuroimaging showcase, as well as quick non-imaging introduction to Nipype workflows.

Basic Concepts

This section will introduce you to all of the key players in Nipype. Basic concepts that you need to learn to fully understand and appreciate Nipype. Once you understand this section, you will know all that you need to know to create any kind of Nipype workflow.

Workflow Examples

In this section, you will find some practical examples and hands-on that show you how to use Nipype in a "real world" scenario.

Advanced Concepts

This section is for more advanced users and Nipype developers.

Useful Resources & Links

This section will give you helpful links and resources so that you always know where to go to learn more.

Home | github | Nipype


You want to help with this tutorial?

Find the github repo of this tutorial under https://github.com/miykael/nipype_tutorial. Feel free to send a pull request or leave an issue with your feedback or ideas.

Home | github | Nipype