Introduction to Neurohacking In R

Johns Hopkins University

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).

100% online courses

Start instantly and learn at your own schedule.

Intermediate Level

Approx. 11 hours to complete

Suggested: 4 weeks of study, 2-4 hours/week

English

Subtitles: English

100% online courses

Start instantly and learn at your own schedule.

Intermediate Level

Approx. 11 hours to complete

Suggested: 4 weeks of study, 2-4 hours/week

English

Subtitles: English

Syllabus - What you will learn from this course

1

Section

1 hour to complete

Introduction

...

3 videos (Total 30 min), 1 reading, 1 quiz

3 videos

Meet the Team6m

Introduction11m

Structural MRI and R12m

1 readings

Syllabus10m

1 practice exercises

Theme 1 Quiz16m

2

Section

2 hours to complete

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 (Total 74 min), 6 quizzes

7 videos

Data Structures and Operations11m

The NIfTI Format9m

Basic Visualization 19m

Basic Visualization 29m

Basic Data Manipulation9m

Transformations and Smoothing14m

Basic MRI Contrasts9m

6 practice exercises

Theme 2 Lecture 1 Quiz10m

Theme 2 Lecture 2 Quiz10m

Theme 2 Lecture 3 Quiz10m

Theme 2 Lecture 4 Quiz10m

Theme 2 Lecture 5 Quiz10m

Theme 2 Lecture 6 Quiz10m

3

Section

3 hours to complete

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 (Total 71 min), 9 quizzes

9 videos

Preprocessing: An Overview14m

Registration15m

fslr: System Requirements8m

Bias Field Correction Using fslr3m

Brain Extraction using fslr5m

Image Registration Using fslr5m

Installing ANTsR5m

Basic Data Manipulation with ANTsR4m

Pre-Processing with ANTSR7m

9 practice exercises

Theme 3 Quiz 110m

Theme 3 Quiz 210m

Theme 3 Quiz 312m

Theme 3 Quiz 410m

Theme 3 Quiz 510m

Theme 3 Quiz 610m

Theme 3 Quiz 710m

Theme 3 Quiz 810m

Theme 3 Quiz 910m

4

Section

3 hours to complete

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 (Total 101 min), 1 reading, 10 quizzes

11 videos

Advanced Brain Image Processing4m

Co-Registration using fslr9m

Co-Registration using ANTsR9m

Wrapper Functions for Processing Pipelines8m

Across-Visit Co-Registration of T1 Images6m

Rigid Registration to a Template8m

Affine Registration of T1 to Template4m

Nonlinear Registration of T1 to Template6m

Getting ROI Anatomic Information from Non-Linear Registration12m

Tissue-Level Segmentation7m

Papayar: Interactively Viewing Images in R22m

1 readings

Papayar Script10m

10 practice exercises

Theme 4 Quiz 110m

Theme 4 Quiz 210m

Theme 4 Quiz 36m

Theme 4 Quiz 410m

Theme 4 Quiz 510m

Theme 4 Quiz 610m

Theme 4 Quiz 710m

Theme 4 Quiz 810m

Theme 4 Quiz 910m

Theme 4 Quiz 1010m

Instructors

Dr. Elizabeth Sweeney

Rice Academy Postdoctoral Fellow

Ciprian M. Crainiceanu

Professor

John Muschelli III

Assistant Scientist

About Johns Hopkins University

The mission of The Johns Hopkins University is to educate its students and cultivate their capacity for life-long learning, to foster independent and original research, and to bring the benefits of discovery to the world....

Frequently Asked Questions

When will I have access to the lectures and assignments?
Once you enroll for a Certificate, you’ll have access to all videos, quizzes, and programming assignments (if applicable). Peer review assignments can only be submitted and reviewed once your session has begun. If you choose to explore the course without purchasing, you may not be able to access certain assignments.
What will I get if I pay for this course?
If you pay for this course, you will have access to all of the features and content you need to earn a Course Certificate. If you complete the course successfully, your electronic Certificate will be added to your Accomplishments page - from there, you can print your Certificate or add it to your LinkedIn profile. Note that the Course Certificate does not represent official academic credit from the partner institution offering the course.
What is the refund policy?
Is financial aid available?
Yes! Coursera provides financial aid to learners who would like to complete a course but cannot afford the course fee. To apply for aid, select "Learn more and apply" in the Financial Aid section below the "Enroll" button. You'll be prompted to complete a simple application; no other paperwork is required.

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Introduction to Neurohacking In R