Important

This guide hasn’t been updated since January 2017 and is based on an older version of Nipype. The code in this guide is not tested against newer Nipype versions and might not work anymore. For a newer, more up to date and better introduction to Nipype, please check out the the Nipype Tutorial.

Table of content

Neuroimaging and Nipype

• Introduction to Nipype
  • What is Nipype?
  • A Short Example
  • Nipype’s Architecture
• Introduction to Neuroimaging
  • Acquisition of MRI Data
  • Specifics of MRI Data
  • Modalities of MRI Data
  • Analysis Steps
• Nipype and Neuroimaging
  • Neuroimaging Workflow
  • Nipype Workflow

Get Nipype to run on your System

• Download and Install Nipype
  • Prepare your System
  • Anaconda
  • NeuroDebian
  • Nipype
• Download and Install Interfaces
  • FSL
  • FreeSurfer
  • MATLAB
  • SPM12
  • ANTs
  • AFNI
  • Additional interfaces
• Clean up your System
• Test your System

First steps with Nipype

• Prepare your Dataset
  • Download the tutorial dataset
  • Make the dataset ready for Nipype
  • Resulting Folder Structure
• How To Build A Pipeline
  • Important building blocks
  • Example preprocessing pipeline
  • Example Script
  • Resulting Folder Structure
  • Common Issues, Problems and Crashes
• How To Visualize A Pipeline
  • What kind of graph do you need?
  • Tweak your visualization
  • Examples of each visualization type

From beginner to expert

• How To Build A Pipeline For A First Level fMRI Analysis
  • Define the structure of your pipeline
  • Write your pipeline script
  • Visualize your pipeline
  • Resulting Folder Structure
• How To Normalize Your Data
  • Normalize Your Data with ANTs
  • Normalize Your Data with SPM12
• How To Build A Pipeline For A Second Level fMRI Analysis
  • Write your pipeline script
  • Visualize your pipeline
  • Resulting Folder Structure

Support

• Help & Support
  • How Nipype Can Help You
  • How to Help Yourself
  • How to Help Me
  • How to Read Crash Files
• Links to Nipype, Programming and Neuroimaging
  • Nipype
  • Programming: Python, Git & more
  • Neuroimaging
• Frequently Asked Questions
  • Basic Statistical Modeling
  • Connectivity
  • Contrasts
  • Coregistration
  • Design
  • HRF
  • Jitter
  • MATLAB Basics
  • Mental Chronometry
  • Normalization
  • P threshold
  • Percent Signal Change
  • Physiology and fMRI
  • ROI
  • Random and Fixed Effects
  • Realignment
  • Scanning
  • Segmentation
  • Slice Timing
  • Smoothing
  • SPM in a Nutshell
  • Temporal Filtering
• Glossary
  • A
  • B
  • C
  • D
  • E
  • F
  • G
  • H
  • I
  • J
  • K
  • L
  • M
  • N
  • O
  • P
  • Q
  • R
  • S
  • T
  • U
  • V
  • W
  • X
  • Y
  • Z
  • Numbers

Downloads

• Download Nipype here: Nipype Homepage.

• Download this beginner’s guide as a PDF here: Nipype Beginner’s Guide

• Download all scripts from this beginner’s guide here: Scripts

• Download the Open fMRI dataset ‘Flanker task (event-related)’ used in this tutorial here: Open fMRI Dataset - ds102