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.
Introduction to Neurohacking In R
Offered By
Introduction to Neurohacking In R
Johns Hopkins University
About this Course
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Learner Career Outcomes
25%
started a new career after completing these courses
11%
got a tangible career benefit from this course
Skills you will gain
Image ProcessingBrainR ProgrammingNeurology
Learner Career Outcomes
25%
started a new career after completing these courses
11%
got a tangible career benefit from this course
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Flexible deadlines
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Intermediate Level
Approx. 12 hours to complete
Suggested: 4 weeks of study, 2-4 hours/week
English
Subtitles: English
Syllabus - What you will learn from this course
1 hour to complete
Introduction
1 hour to complete
3 videos (Total 30 min), 1 reading, 1 quiz
1 reading
Syllabus10m
1 practice exercise
Theme 1 Quiz16m
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.
2 hours to complete
7 videos (Total 74 min)
7 videos
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 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.
3 hours to complete
9 videos (Total 71 min)
9 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
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
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.
3 hours to complete
11 videos (Total 101 min), 1 reading, 10 quizzes
11 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
1 reading
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
Reviews
4.6
TOP REVIEWS FROM INTRODUCTION TO NEUROHACKING IN R
by BRFeb 8, 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 SJMay 7, 2019
Thank you for the wonderful course. Especially useful when the team explains every new line of code. As a current undergraduate and aspiring neuroscience researcher, this is tremendously helpful.
by ANJul 17, 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!
by HEDec 16, 2019
A very useful and informative course. An organized, well prepared, and focused course. Thanks to the fabulous team. I learned a lot of stuff related to neuroimaging.
by JSJan 18, 2017
It would have been better if there were practical exercises, nevertheless it was very comprehensive for basic procedures of fMRI analysis.
by SAAug 19, 2019
it would be great if can create a specialization for this course going in more depth like making your own dti films etc.
by MTApr 4, 2018
Great concise walk-through of neuro-imaging techniques. Low quality audio and a lot of background noise though.
by ASAug 25, 2017
I am really appreciate this course. Its good to have a structured course on these complex topics.
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.
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