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Introduction to Neurohacking In R
  • Level Professional
  • Duration 18 hours
  • Course by Johns Hopkins University
  • Offered by

About

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).

Modules

Welcome to the Course

    • 1 Videos
    • 1 Readings
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1 Videos

  • Meet the Team

1 Readings

  • Syllabus

1.1 Neurohacking and Neuroimaging

    • 2 Videos
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2 Videos

  • Introduction
  • Structural MRI and R

Theme 1 Quiz

    • 1 Assignment
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1 Assignment

  • Theme 1 Quiz

2.1 Data Structures and Operations

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 2 Lecture 1 Quiz

1 Videos

  • Data Structures and Operations

2.2 The NIfTI Format

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 2 Lecture 2 Quiz

1 Videos

  • The NIfTI Format

2.3 Basic Visualization

    • 2 Videos
    • 1 Assignment
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1 Assignment

  • Theme 2 Lecture 3 Quiz

2 Videos

  • Basic Visualization 1
  • Basic Visualization 2

2.4 Basic Data Manipulation

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 2 Lecture 4 Quiz

1 Videos

  • Basic Data Manipulation

2.5 Transformations and Smoothing

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 2 Lecture 5 Quiz

1 Videos

  • Transformations and Smoothing

2.6 Basic MRI Contrasts

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 2 Lecture 6 Quiz

1 Videos

  • Basic MRI Contrasts

3.1 Preprocessing

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 1

1 Videos

  • Preprocessing: An Overview

3.2 Image Registration: Background

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 2

1 Videos

  • Registration

3.3 fslr: System Requirements

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 3

1 Videos

  • fslr: System Requirements

3.4 Inhomogeneity Correction using fslr

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 4

1 Videos

  • Bias Field Correction Using fslr

3.5 Brain Extraction Using fslr

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 5

1 Videos

  • Brain Extraction using fslr

3.6 Image Registration Using fslr

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 6

1 Videos

  • Image Registration Using fslr

3.7 ANTsR: R Package Wrapper for ANTs

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 7

1 Videos

  • Installing ANTsR

3.8 Basic Data Manipulation with ANTsR

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 8

1 Videos

  • Basic Data Manipulation with ANTsR

3.9 Pre-Processing with ANTSR

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 3 Quiz 9

1 Videos

  • Pre-Processing with ANTSR

4.1 Image Registration: Extensions

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 1

1 Videos

  • Advanced Brain Image Processing

4.2 FSLR Co-Registration

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 2

1 Videos

  • Co-Registration using fslr

4.3 ANTSR Co-Registration

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 3

1 Videos

  • Co-Registration using ANTsR

4.4 Wrapper Functions for Processing Pipelines

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 4

1 Videos

  • Wrapper Functions for Processing Pipelines

4.5 Across-Visit Co-Registration of T1 Images

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 5

1 Videos

  • Across-Visit Co-Registration of T1 Images

4.6 Rigid Registration to a Template

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 6

1 Videos

  • Rigid Registration to a Template

4.7 Affine Registration of T1 to Template

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 7

1 Videos

  • Affine Registration of T1 to Template

4.8 Nonlinear Registration of T1 to Template

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 8

1 Videos

  • Nonlinear Registration of T1 to Template

4.9 Getting ROI Anatomic Information from Non-Linear Registration

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 9

1 Videos

  • Getting ROI Anatomic Information from Non-Linear Registration

4.10 Tissue-Level Segmentation

    • 1 Videos
    • 1 Assignment
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1 Assignment

  • Theme 4 Quiz 10

1 Videos

  • Tissue-Level Segmentation

Bonus Lesson: Papayar: Interactively Viewing Images in R

    • 1 Videos
    • 1 Readings
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1 Videos

  • Papayar: Interactively Viewing Images in R

1 Readings

  • Papayar Script

Auto Summary

Discover the world of Neurohacking with R in this professional course focused on Big Data and Analytics. Led by Coursera, you'll master the manipulation, processing, and analysis of neuroimaging data, specifically structural MRI. Key skills include reading/writing NIfTI images, visualization, inhomogeneity correction, brain extraction, and image registration. Perfect for professionals, this 1080-minute course is available with a Starter subscription.

Dr. Elizabeth Sweeney
Instructors

Dr. Elizabeth Sweeney

Ciprian M. Crainiceanu
Instructors

Ciprian M. Crainiceanu

John Muschelli III
Instructors

John Muschelli III