Informações sobre o curso
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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curso 100% online

Comece imediatamente e aprenda em seu próprio cronograma.
Intermediate Level

Nível intermediário

Clock

Aprox. 11 horas restantes

Sugerido: 4 weeks of study, 2-4 hours/week
Comment Dots

English

Legendas: English
Globe

curso 100% online

Comece imediatamente e aprenda em seu próprio cronograma.
Intermediate Level

Nível intermediário

Clock

Aprox. 11 horas restantes

Sugerido: 4 weeks of study, 2-4 hours/week
Comment Dots

English

Legendas: English

Syllabus - What you will learn from this course

1

Section
Clock
1 hour to complete

Introduction

...
Reading
3 videos (Total 30 min), 1 reading, 1 quiz
Video3 videos
Introduction11m
Structural MRI and R12m
Reading1 readings
Syllabus10m
Quiz1 practice exercises
Theme 1 Quiz16m

2

Section
Clock
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....
Reading
7 videos (Total 74 min), 6 quizzes
Video7 videos
The NIfTI Format9m
Basic Visualization 19m
Basic Visualization 29m
Basic Data Manipulation9m
Transformations and Smoothing14m
Basic MRI Contrasts9m
Quiz6 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
Clock
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....
Reading
9 videos (Total 71 min), 9 quizzes
Video9 videos
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
Quiz9 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
Clock
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....
Reading
11 videos (Total 101 min), 1 reading, 10 quizzes
Video11 videos
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
Reading1 readings
Papayar Script10m
Quiz10 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
4.6

Top Reviews

By BRFeb 9th 2017

I like that this course goes through most necessary steps, my only suggest would be to have one additional week where you go through everything all together, and then do some simple group analysis.

By ANJul 18th 2017

Perfect! Precise to the subject and provides a lot of hands-on details, which is, unfortunately, something that most other similar courses don't do. Absolutely loved it!

Instructors

Avatar

Dr. Elizabeth Sweeney

Rice Academy Postdoctoral Fellow
Avatar

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

  • 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.

  • 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.

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