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).
Introduction to Neurohacking In R
ofrecido por
Johns Hopkins University
Acerca de este Curso
4.6
141 calificaciones
Habilidades que obtendrás
Image ProcessingBrainR ProgrammingNeurology
Programa - Qué aprenderás en este curso
Semana
1Introduction
3 videos (Total 30 min), 1 reading, 1 quiz
1 lectura
Syllabus10m
1 ejercicio de práctica
Theme 1 Quiz16m
Semana
2Neuroimaging: 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
The NIfTI Format9m
Basic Visualization 19m
Basic Visualization 29m
Basic Data Manipulation9m
Transformations and Smoothing14m
Basic MRI Contrasts9m
6 ejercicios de práctica
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
Semana
3Image 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
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 ejercicios de práctica
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
Semana
4Extended 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
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 lectura
Papayar Script10m
10 ejercicios de práctica
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
Principales revisiones
por BR•Feb 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.
por AN•Jul 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!
Instructores
Dr. Elizabeth Sweeney
Rice Academy Postdoctoral FellowBiostatistics
Ciprian M. Crainiceanu
ProfessorBiostatstics
John Muschelli III
Assistant ScientistBiostatistics
Acerca de 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.
Preguntas Frecuentes
¿Cuándo podré acceder a las lecciones y tareas?
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¿Qué recibiré si compro el Certificado?
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