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Johns Hopkins University

Introduction to Neurohacking In R

Johns Hopkins University via Coursera

Overview

Neurohacking describes how to use the R programming language (https://cran.r-project.org/) and its associated package to perform manipulation, processing, and analysis of neuroimaging data. We focus on publicly-available structural magnetic resonance imaging (MRI). We discuss concepts such as inhomogeneity correction, image registration, and image visualization.

By the end of this course, you will be able to:

Read/write images of the brain in the NIfTI (Neuroimaging Informatics Technology Initiative) format
Visualize and explore these images
Perform inhomogeneity correction, brain extraction, and image registration (within a subject and to a template).

Syllabus

  • Introduction
  • Neuroimaging: Formats and Visualization
    • In this section, we will discuss different formats that brain images come in, as well as some of the commonly done magnetic resonance imaging (MRI) scans.
  • Image Processing
    • In this section, we will discuss the steps done to process brain MRI data. We will discuss inhomogeneity correction, brain extraction or skull stripping, and various image registration techniques.
  • Extended Image Processing
    • In this section, we will discuss the different types of registration and how one would go through processing a multi-sequence MRI scan, as well as wrapper functions that make the process much easier. We also cover interactive exploration of brain image data and tissue-level (white/gray matter and cerebrospinal fluid (CSF)) segmentation from a T1-weighted image.

Taught by

Dr. Elizabeth Sweeney , Ciprian M. Crainiceanu and John Muschelli III

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