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.
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.
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.
In this section, you will find some practical examples and hands-on that show you how to use Nipype in a "real world" scenario.
This section is for more advanced users and Nipype developers.
This section will give you helpful links and resources so that you always know where to go to learn more.