index.ipynb

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       "<style>.container { width:75% !important; }</style>\n",
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       "        \n",
       "<body>\n",
       "  <article id=\"homepage\">\n",
       "    <a id=\"library-section\"></a>\n",
       "    <div class=\"library-section\">\n",
       "      <div class=\"section-separator library-section-separator\">\n",
       "        <center><img src=\"static/images/logoNipype_tutorial.png\" width=700></center>\n",
       "        <p>Welcome to the Nipype Tutorial! It covers the basic concepts and most common use cases of Nipype and will teach\n",
       "            you everything so that you can start creating your own workflows in no time. We recommend that you start with\n",
       "            the introduction section to familiarize yourself with the tools used in this tutorial and then move on to the\n",
       "            basic concepts section to learn everything you need to know for your everyday life with Nipype. The workflow\n",
       "            examples section shows you a real example of how you can use Nipype to analyze an actual dataset. For a very \n",
       "            quick non-imaging introduction, you can check the Nipype Quickstart notebooks in the introduction section.\n",
       "            </p><p>\n",
       "            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>.\n",
       "            But if you want to have the real experience and want to go through the computations by yourself, we highly\n",
       "            recommend you to use a Docker container. More about the Docker image that can be used to run the tutorial can be found \n",
       "            <a href=\"https://miykael.github.io/nipype_tutorial/notebooks/introduction_docker.html\">here</a>.\n",
       "            This docker container gives you the opportunity to adapt the commands to your liking and discover the flexibility and real power of\n",
       "            Nipype yourself.\n",
       "            </p><p>\n",
       "            To run the tutorial locally on your system, we will use a <a href=\"http://www.docker.com/\">Docker</a> container. For this you\n",
       "            need to install Docker and download a docker image that provides you a neuroimaging environment based on a Debian system,\n",
       "            with working Python 3 software (including Nipype, dipy, matplotlib, nibabel, nipy, numpy, pandas, scipy, seaborn and more),\n",
       "            FSL, ANTs and SPM12 (no license needed). We used <a href=\"https://github.com/kaczmarj/neurodocker\">Neurodocker</a> to create this docker image.\n",
       "            </p><p>\n",
       "            If you do not want to run the tutorial locally, you can also use \n",
       "            <a href=\"https://mybinder.org/v2/gh/miykael/nipype_tutorial/master\">Binder service</a>. \n",
       "            Binder automatically launches the Docker container for you and you have access to all of the notebooks. \n",
       "            Note, that Binder provides between 1G and 4G RAM memory, some notebooks from Workflow Examples might not work. \n",
       "            All notebooks from Introduction and Basic Concepts parts should work.\n",
       "           </p><p>\n",
       "            For everything that isn't covered in this tutorial, check out the <a href=\"http://nipype.readthedocs.io/en/latest/\">main homepage</a>.\n",
       "            And if you haven't had enough and want to learn even more about Nipype and Neuroimaging, make sure to look at\n",
       "            the <a href=\"https://miykael.github.io/nipype-beginner-s-guide/\">detailed beginner's guide</a>.\n",
       "            </p>\n",
       "      </div>\n",
       "\n",
       "      <!--Comment: to change the color of the title or section, change the second h2 class argument and the third div\n",
       "            argument to either color01, color02, ... color06 or color07-->\n",
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       "       For example, to have three columns, change the value to 'pure-u-1-3'-->\n",
       "\n",
       "      <h2 class=\"domain-header color01\"><a class=\"domain-title\">Introduction</a></h2>\n",
       "      <div class=\"pure-g domain-table-container color01\">\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_nipype.html\">Nipype</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_jupyter-notebook.ipynb\">Jupyter-Notebook</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_dataset.ipynb\">BIDS & Tutorial Dataset</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_docker.ipynb\">Docker</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_neurodocker.ipynb\">Neurodocker</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_python.ipynb\">Python</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_showcase.ipynb\">Nipype Showcase</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_quickstart.ipynb\">Nipype Quickstart</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_quickstart_non-neuroimaging.ipynb\">Nipype Quickstart (non-neuroimaging examples)</a>\n",
       "      </div>\n",
       "      <p>This section is meant as a general overview. It should give you a short introduction to the main topics that\n",
       "          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>\n",
       "\n",
       "      <h2 class=\"domain-header color02\"><a class=\"domain-title\">Basic Concepts</a></h2>\n",
       "      <div class=\"pure-g domain-table-container color02\">\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_interfaces.ipynb\">Interfaces</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_nodes.ipynb\">Nodes</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_workflow.ipynb\">Workflow</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_graph_visualization.ipynb\">Graph Visualization</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_data_input.ipynb\">Data Input</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_data_input_bids.ipynb\">Data Input with BIDS</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_data_output.ipynb\">Data Output</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_plugins.ipynb\">Execution Plugins</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_function_interface.ipynb\">Function Interface</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_iteration.ipynb\">Iteration / Iterables</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_mapnodes.ipynb\">MapNodes</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_joinnodes.ipynb\">JoinNode, synchronize & itersource</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_error_and_crashes.ipynb\">Errors & Crashes</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_debug.ipynb\">Debugging Nipype Workflows</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_model_specification_fmri.ipynb\">fMRI Model Specification</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_execution_configuration.ipynb\">Execution Configuration</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_import_workflows.ipynb\">Import existing Workflows</a>\n",
       "      </div>\n",
       "      <p>This section will introduce you to all of the key players in Nipype. Basic concepts that you need to learn to\n",
       "          fully understand and appreciate Nipype. Once you understand this section, you will know all that you need to know\n",
       "          to create any kind of Nipype workflow.</p>\n",
       "\n",
       "      <h2 class=\"domain-header color03\"><a class=\"domain-title\">Workflow Examples</a></h2>\n",
       "      <div class=\"pure-g domain-table-container color03\">\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_preprocessing.ipynb\">Example 1: Preprocessing</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_1stlevel.ipynb\">Example 1: 1st-level Analysis</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_normalize.ipynb\">Example 1: Normalize Data</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_2ndlevel.ipynb\">Example 1: 2nd-level Analysis</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/handson_preprocessing.ipynb\">Hands-on 1: Preprocessing</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/handson_analysis.ipynb\">Hands-on 1: Analysis</a>\n",
       "      </div>\n",
       "      <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>\n",
       "\n",
       "      <h2 class=\"domain-header color04\"><a class=\"domain-title\">Advanced Concepts</a></h2>\n",
       "      <div class=\"pure-g domain-table-container color04\">\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_create_interfaces.ipynb\">Create Interfaces</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_interfaces_caching.ipynb\">Interfaces Caching</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_command_line_interface.ipynb\">Nipype Command Line Interface</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_aws.ipynb\">Amazon Web Services (AWS)</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_sphinx_ext.ipynb\">Sphinx extensions</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_spmmcr.ipynb\">SPM with MATLAB Common Runtime (MCR)</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_mipav.ipynb\">Using MIPAV, JIST, and CBS Tools</a>      </div>\n",
       "      <p>This section is for more advanced users and Nipype developers.</p>\n",
       "\n",
       "      <h2 class=\"domain-header color05\"><a class=\"domain-title\">Useful Resources & Links</a></h2>\n",
       "      <div class=\"pure-g domain-table-container color05\">\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_installation.ipynb\">Install Nipype</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_resources.ipynb\">Useful Resources & Links</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_help.ipynb\">Where to find Help</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_python_cheat_sheet.ipynb\">Python Cheat Sheet</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://nipype.readthedocs.io/en/latest/\">Nipype (main homepage)</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://miykael.github.io/nipype-beginner-s-guide/\">Nipype Beginner's Guide</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://github.com/miykael/nipype_tutorial\">Github of Nipype Tutorial</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://github.com/kaczmarj/neurodocker\">Neurodocker</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://nipy.org/nibabel/\">NiBabel</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://nilearn.github.io/\">Nilearn</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://openneuro.org/\">OpenNeuro</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://bids-apps.neuroimaging.io\">BIDS Apps</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://fmriprep.readthedocs.io/en/latest/index.html\">fmriprep</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://mriqc.readthedocs.io/en/latest/#\">MRIQC</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://mindboggle.info/\">Mindboggle</a>\n",
       "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://timvanmourik.github.io/Porcupine/\">PORcupine</a>\n",
       "      </div>\n",
       "      <p>This section will give you helpful links and resources so that you always know where to go to learn more.</p>\n",
       "\n",
       "    </div>\n",
       "  </article>\n",
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       "\n",
       "<hr/>\n",
       "\n",
       "<h2>You want to help with this tutorial?</h2>\n",
       "<p>Find the github repo of this tutorial under <a href=\"https://github.com/miykael/nipype_tutorial\">https://github.com/miykael/nipype_tutorial</a>.\n",
       "    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.\n",
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    " <!–– TUTORIAL USERS: PLEASE EXECUTE THIS CELL ––>\n",
    "\n",
    "<style>.container { width:75% !important; }</style>\n",
    "<link rel='stylesheet' type='text/css' href='static/css/mobile.css'>\n",
    "<link rel='stylesheet' type='text/css' href='static/css/homepage.css'>\n",
    "        \n",
    "<body>\n",
    "  <article id=\"homepage\">\n",
    "    <a id=\"library-section\"></a>\n",
    "    <div class=\"library-section\">\n",
    "      <div class=\"section-separator library-section-separator\">\n",
    "        <center><img src=\"static/images/logoNipype_tutorial.png\" width=700></center>\n",
    "        <p>Welcome to the Nipype Tutorial! It covers the basic concepts and most common use cases of Nipype and will teach\n",
    "            you everything so that you can start creating your own workflows in no time. We recommend that you start with\n",
    "            the introduction section to familiarize yourself with the tools used in this tutorial and then move on to the\n",
    "            basic concepts section to learn everything you need to know for your everyday life with Nipype. The workflow\n",
    "            examples section shows you a real example of how you can use Nipype to analyze an actual dataset. For a very \n",
    "            quick non-imaging introduction, you can check the Nipype Quickstart notebooks in the introduction section.\n",
    "            </p><p>\n",
    "            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>.\n",
    "            But if you want to have the real experience and want to go through the computations by yourself, we highly\n",
    "            recommend you to use a Docker container. More about the Docker image that can be used to run the tutorial can be found \n",
    "            <a href=\"https://miykael.github.io/nipype_tutorial/notebooks/introduction_docker.html\">here</a>.\n",
    "            This docker container gives you the opportunity to adapt the commands to your liking and discover the flexibility and real power of\n",
    "            Nipype yourself.\n",
    "            </p><p>\n",
    "            To run the tutorial locally on your system, we will use a <a href=\"http://www.docker.com/\">Docker</a> container. For this you\n",
    "            need to install Docker and download a docker image that provides you a neuroimaging environment based on a Debian system,\n",
    "            with working Python 3 software (including Nipype, dipy, matplotlib, nibabel, nipy, numpy, pandas, scipy, seaborn and more),\n",
    "            FSL, ANTs and SPM12 (no license needed). We used <a href=\"https://github.com/kaczmarj/neurodocker\">Neurodocker</a> to create this docker image.\n",
    "            </p><p>\n",
    "            If you do not want to run the tutorial locally, you can also use \n",
    "            <a href=\"https://mybinder.org/v2/gh/miykael/nipype_tutorial/master\">Binder service</a>. \n",
    "            Binder automatically launches the Docker container for you and you have access to all of the notebooks. \n",
    "            Note, that Binder provides between 1G and 4G RAM memory, some notebooks from Workflow Examples might not work. \n",
    "            All notebooks from Introduction and Basic Concepts parts should work.\n",
    "           </p><p>\n",
    "            For everything that isn't covered in this tutorial, check out the <a href=\"http://nipype.readthedocs.io/en/latest/\">main homepage</a>.\n",
    "            And if you haven't had enough and want to learn even more about Nipype and Neuroimaging, make sure to look at\n",
    "            the <a href=\"https://miykael.github.io/nipype-beginner-s-guide/\">detailed beginner's guide</a>.\n",
    "            </p>\n",
    "      </div>\n",
    "\n",
    "      <!--Comment: to change the color of the title or section, change the second h2 class argument and the third div\n",
    "            argument to either color01, color02, ... color06 or color07-->\n",
    "\n",
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    "       For example, to have three columns, change the value to 'pure-u-1-3'-->\n",
    "\n",
    "      <h2 class=\"domain-header color01\"><a class=\"domain-title\">Introduction</a></h2>\n",
    "      <div class=\"pure-g domain-table-container color01\">\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_nipype.html\">Nipype</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_jupyter-notebook.ipynb\">Jupyter-Notebook</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_dataset.ipynb\">BIDS & Tutorial Dataset</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_docker.ipynb\">Docker</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_neurodocker.ipynb\">Neurodocker</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_python.ipynb\">Python</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_showcase.ipynb\">Nipype Showcase</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_quickstart.ipynb\">Nipype Quickstart</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/introduction_quickstart_non-neuroimaging.ipynb\">Nipype Quickstart (non-neuroimaging examples)</a>\n",
    "      </div>\n",
    "      <p>This section is meant as a general overview. It should give you a short introduction to the main topics that\n",
    "          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>\n",
    "\n",
    "      <h2 class=\"domain-header color02\"><a class=\"domain-title\">Basic Concepts</a></h2>\n",
    "      <div class=\"pure-g domain-table-container color02\">\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_interfaces.ipynb\">Interfaces</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_nodes.ipynb\">Nodes</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_workflow.ipynb\">Workflow</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_graph_visualization.ipynb\">Graph Visualization</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_data_input.ipynb\">Data Input</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_data_input_bids.ipynb\">Data Input with BIDS</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_data_output.ipynb\">Data Output</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_plugins.ipynb\">Execution Plugins</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_function_interface.ipynb\">Function Interface</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_iteration.ipynb\">Iteration / Iterables</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_mapnodes.ipynb\">MapNodes</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_joinnodes.ipynb\">JoinNode, synchronize & itersource</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_error_and_crashes.ipynb\">Errors & Crashes</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_debug.ipynb\">Debugging Nipype Workflows</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_model_specification_fmri.ipynb\">fMRI Model Specification</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_execution_configuration.ipynb\">Execution Configuration</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/basic_import_workflows.ipynb\">Import existing Workflows</a>\n",
    "      </div>\n",
    "      <p>This section will introduce you to all of the key players in Nipype. Basic concepts that you need to learn to\n",
    "          fully understand and appreciate Nipype. Once you understand this section, you will know all that you need to know\n",
    "          to create any kind of Nipype workflow.</p>\n",
    "\n",
    "      <h2 class=\"domain-header color03\"><a class=\"domain-title\">Workflow Examples</a></h2>\n",
    "      <div class=\"pure-g domain-table-container color03\">\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_preprocessing.ipynb\">Example 1: Preprocessing</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_1stlevel.ipynb\">Example 1: 1st-level Analysis</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_normalize.ipynb\">Example 1: Normalize Data</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/example_2ndlevel.ipynb\">Example 1: 2nd-level Analysis</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/handson_preprocessing.ipynb\">Hands-on 1: Preprocessing</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/handson_analysis.ipynb\">Hands-on 1: Analysis</a>\n",
    "      </div>\n",
    "      <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>\n",
    "\n",
    "      <h2 class=\"domain-header color04\"><a class=\"domain-title\">Advanced Concepts</a></h2>\n",
    "      <div class=\"pure-g domain-table-container color04\">\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_create_interfaces.ipynb\">Create Interfaces</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_interfaces_caching.ipynb\">Interfaces Caching</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_command_line_interface.ipynb\">Nipype Command Line Interface</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_aws.ipynb\">Amazon Web Services (AWS)</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_sphinx_ext.ipynb\">Sphinx extensions</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_spmmcr.ipynb\">SPM with MATLAB Common Runtime (MCR)</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/advanced_mipav.ipynb\">Using MIPAV, JIST, and CBS Tools</a>      </div>\n",
    "      <p>This section is for more advanced users and Nipype developers.</p>\n",
    "\n",
    "      <h2 class=\"domain-header color05\"><a class=\"domain-title\">Useful Resources & Links</a></h2>\n",
    "      <div class=\"pure-g domain-table-container color05\">\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_installation.ipynb\">Install Nipype</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_resources.ipynb\">Useful Resources & Links</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_help.ipynb\">Where to find Help</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"notebooks/resources_python_cheat_sheet.ipynb\">Python Cheat Sheet</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://nipype.readthedocs.io/en/latest/\">Nipype (main homepage)</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://miykael.github.io/nipype-beginner-s-guide/\">Nipype Beginner's Guide</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://github.com/miykael/nipype_tutorial\">Github of Nipype Tutorial</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://github.com/kaczmarj/neurodocker\">Neurodocker</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://nipy.org/nibabel/\">NiBabel</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://nilearn.github.io/\">Nilearn</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://openneuro.org/\">OpenNeuro</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://bids-apps.neuroimaging.io\">BIDS Apps</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"http://fmriprep.readthedocs.io/en/latest/index.html\">fmriprep</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://mriqc.readthedocs.io/en/latest/#\">MRIQC</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://mindboggle.info/\">Mindboggle</a>\n",
    "        <a class=\"subject-link pure-u-1-4\" target=\"_blank\" href=\"https://timvanmourik.github.io/Porcupine/\">PORcupine</a>\n",
    "      </div>\n",
    "      <p>This section will give you helpful links and resources so that you always know where to go to learn more.</p>\n",
    "\n",
    "    </div>\n",
    "  </article>\n",
    "</body>\n",
    "\n",
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    "\n",
    "<hr/>\n",
    "\n",
    "<h2>You want to help with this tutorial?</h2>\n",
    "<p>Find the github repo of this tutorial under <a href=\"https://github.com/miykael/nipype_tutorial\">https://github.com/miykael/nipype_tutorial</a>.\n",
    "    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.\n",
    "</p>\n",
    "To inspect the html code of this page, click: <form action=\"javascript:code_toggle()\"><input type=\"submit\" value=\"Show HTML code\"></form>"
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