Introduction to Neurohacking In R

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Introduction to Neurohacking In R

This course is part of Neuroscience and Neuroimaging Specialization

Instructors: Dr. Elizabeth Sweeney

25,658 already enrolled

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4 modules

Gain insight into a topic and learn the fundamentals.

315 reviews

Intermediate level

Some related experience required

Flexible schedule

2 weeks at 10 hours a week

Learn at your own pace

94%

Most learners liked this course

4 modules

Gain insight into a topic and learn the fundamentals.

315 reviews

Intermediate level

Some related experience required

Flexible schedule

2 weeks at 10 hours a week

Learn at your own pace

94%

Most learners liked this course

Skills you'll gain

Tools you'll learn

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Shareable certificate

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Assessments

26 assignments

Taught in English

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This course is part of the Neuroscience and Neuroimaging Specialization

When you enroll in this course, you'll also be enrolled in this Specialization.

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There are 4 modules in 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.

What's included

3 videos1 reading1 assignment

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.

What's included

7 videos6 assignments

7 videosTotal 74 minutes

Data Structures and Operations12 minutes
The NIfTI Format10 minutes
Basic Visualization 19 minutes
Basic Visualization 210 minutes
Basic Data Manipulation10 minutes
Transformations and Smoothing15 minutes
Basic MRI Contrasts9 minutes

6 assignmentsTotal 180 minutes

Theme 2 Lecture 1 Quiz30 minutes
Theme 2 Lecture 2 Quiz30 minutes
Theme 2 Lecture 3 Quiz30 minutes
Theme 2 Lecture 4 Quiz30 minutes
Theme 2 Lecture 5 Quiz30 minutes
Theme 2 Lecture 6 Quiz30 minutes

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.

What's included

9 videos9 assignments

9 videosTotal 71 minutes

Preprocessing: An Overview14 minutes
Registration15 minutes
fslr: System Requirements9 minutes
Bias Field Correction Using fslr4 minutes
Brain Extraction using fslr6 minutes
Image Registration Using fslr6 minutes
Installing ANTsR5 minutes
Basic Data Manipulation with ANTsR5 minutes
Pre-Processing with ANTSR8 minutes

9 assignmentsTotal 270 minutes

Theme 3 Quiz 130 minutes
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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.

What's included

11 videos1 reading10 assignments

11 videosTotal 101 minutes

Advanced Brain Image Processing5 minutes
Co-Registration using fslr9 minutes
Co-Registration using ANTsR10 minutes
Wrapper Functions for Processing Pipelines8 minutes
Across-Visit Co-Registration of T1 Images6 minutes
Rigid Registration to a Template8 minutes
Affine Registration of T1 to Template4 minutes
Nonlinear Registration of T1 to Template7 minutes
Getting ROI Anatomic Information from Non-Linear Registration13 minutes
Tissue-Level Segmentation7 minutes
Papayar: Interactively Viewing Images in R23 minutes

1 readingTotal 10 minutes

Papayar Script10 minutes

10 assignmentsTotal 300 minutes

Theme 4 Quiz 130 minutes
Theme 4 Quiz 230 minutes
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Theme 4 Quiz 530 minutes
Theme 4 Quiz 630 minutes
Theme 4 Quiz 730 minutes
Theme 4 Quiz 830 minutes
Theme 4 Quiz 930 minutes
Theme 4 Quiz 1030 minutes

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Instructors

Instructor ratings

(50 ratings)

Dr. Elizabeth Sweeney

Johns Hopkins University

1 Course25,658 learners

Offered by

Johns Hopkins University

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Showing 3 of 315

Reviewed on Apr 4, 2018

Great concise walk-through of neuro-imaging techniques. Low quality audio and a lot of background noise though.

Reviewed on Aug 25, 2017

I am really appreciate this course. Its good to have a structured course on these complex topics.

Reviewed on Dec 5, 2023

excellent course building you up with basics using R and fsl, antr

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