Introduction to Neurohacking In R

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Description

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About this course: 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).

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When you enroll for courses through Coursera you get to choose for a paid plan or for a free plan

  • Free plan: No certicification and/or audit only. You will have access to all course materials except graded items.
  • Paid plan: Commit to earning a Certificate—it's a trusted, shareable way to showcase your new skills.

About this course: 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).

Created by:  Johns Hopkins University
  • Taught by:  Dr. Elizabeth Sweeney , Rice Academy Postdoctoral Fellow

    Biostatistics
  • Taught by:  Ciprian M. Crainiceanu, Professor

    Biostatstics
  • Taught by:  John Muschelli III , Assistant Scientist

    Biostatistics
Level Intermediate Commitment 4 weeks of study, 2-4 hours/week Language English How To Pass Pass all graded assignments to complete the course. User Ratings 4.6 stars Average User Rating 4.6See what learners said Coursework

Each course is like an interactive textbook, featuring pre-recorded videos, quizzes and projects.

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Syllabus


WEEK 1


Introduction



3 videos, 1 reading, 1 practice quiz expand


  1. Video: Meet the Team
  2. Reading: Syllabus
  3. Video: Introduction
  4. Video: Structural MRI and R
  5. Practice Quiz: Theme 1 Quiz


WEEK 2


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.


7 videos expand


  1. Video: Data Structures and Operations
  2. Video: The NIfTI Format
  3. Video: Basic Visualization 1
  4. Video: Basic Visualization 2
  5. Video: Basic Data Manipulation
  6. Video: Transformations and Smoothing
  7. Video: Basic MRI Contrasts

Graded: Theme 2 Lecture 1 Quiz
Graded: Theme 2 Lecture 2 Quiz
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Graded: Theme 2 Lecture 4 Quiz
Graded: Theme 2 Lecture 5 Quiz
Graded: Theme 2 Lecture 6 Quiz

WEEK 3


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.


9 videos expand


  1. Video: Preprocessing: An Overview
  2. Video: Registration
  3. Video: fslr: System Requirements
  4. Video: Bias Field Correction Using fslr
  5. Video: Brain Extraction using fslr
  6. Video: Image Registration Using fslr
  7. Video: Installing ANTsR
  8. Video: Basic Data Manipulation with ANTsR
  9. Video: Pre-Processing with ANTSR

Graded: Theme 3 Quiz 1
Graded: Theme 3 Quiz 2
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Graded: Theme 3 Quiz 9

WEEK 4


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.


11 videos, 1 reading expand


  1. Video: Advanced Brain Image Processing
  2. Video: Co-Registration using fslr
  3. Video: Co-Registration using ANTsR
  4. Video: Wrapper Functions for Processing Pipelines
  5. Video: Across-Visit Co-Registration of T1 Images
  6. Video: Rigid Registration to a Template
  7. Video: Affine Registration of T1 to Template
  8. Video: Nonlinear Registration of T1 to Template
  9. Video: Getting ROI Anatomic Information from Non-Linear Registration
  10. Video: Tissue-Level Segmentation
  11. Video: Papayar: Interactively Viewing Images in R
  12. Reading: Papayar Script

Graded: Theme 4 Quiz 1
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Graded: Theme 4 Quiz 10
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