À propos de ce cours : 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).
Créé par : Johns Hopkins University
Enseigné par : Dr. Elizabeth Sweeney , Rice Academy Postdoctoral Fellow
BiostatisticsEnseigné par : Ciprian M. Crainiceanu, Professor
BiostatsticsEnseigné par : John Muschelli III , Assistant Scientist
Biostatistics
| Niveau | Intermédiaire |
| Engagement | 4 weeks of study, 2-4 hours/week |
| Langue | English |
| Comment réussir | Réussissez tous les devoirs notés pour terminer le cours. |
| Notes des utilisateurs |
Programme de cours
SEMAINE 1
Introduction
3 vidéos, 1 lecture, 1 quiz pour s'exercer
- Reading: Syllabus
- Vidéo: Introduction
- Vidéo: Structural MRI and R
- Practice Quiz: Theme 1 Quiz
SEMAINE 2
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 vidéos
- Vidéo: The NIfTI Format
- Vidéo: Basic Visualization 1
- Vidéo: Basic Visualization 2
- Vidéo: Basic Data Manipulation
- Vidéo: Transformations and Smoothing
- Vidéo: Basic MRI Contrasts
Noté: Theme 2 Lecture 1 Quiz
Noté: Theme 2 Lecture 2 Quiz
Noté: Theme 2 Lecture 3 Quiz
Noté: Theme 2 Lecture 4 Quiz
Noté: Theme 2 Lecture 5 Quiz
Noté: Theme 2 Lecture 6 Quiz
SEMAINE 3
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 vidéos
- Vidéo: Registration
- Vidéo: fslr: System Requirements
- Vidéo: Bias Field Correction Using fslr
- Vidéo: Brain Extraction using fslr
- Vidéo: Image Registration Using fslr
- Vidéo: Installing ANTsR
- Vidéo: Basic Data Manipulation with ANTsR
- Vidéo: Pre-Processing with ANTSR
Noté: Theme 3 Quiz 1
Noté: Theme 3 Quiz 2
Noté: Theme 3 Quiz 3
Noté: Theme 3 Quiz 4
Noté: Theme 3 Quiz 5
Noté: Theme 3 Quiz 6
Noté: Theme 3 Quiz 7
Noté: Theme 3 Quiz 8
Noté: Theme 3 Quiz 9
SEMAINE 4
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 vidéos, 1 lecture
- Vidéo: Co-Registration using fslr
- Vidéo: Co-Registration using ANTsR
- Vidéo: Wrapper Functions for Processing Pipelines
- Vidéo: Across-Visit Co-Registration of T1 Images
- Vidéo: Rigid Registration to a Template
- Vidéo: Affine Registration of T1 to Template
- Vidéo: Nonlinear Registration of T1 to Template
- Vidéo: Getting ROI Anatomic Information from Non-Linear Registration
- Vidéo: Tissue-Level Segmentation
- Vidéo: Papayar: Interactively Viewing Images in R
- Reading: Papayar Script
Noté: Theme 4 Quiz 1
Noté: Theme 4 Quiz 2
Noté: Theme 4 Quiz 3
Noté: Theme 4 Quiz 4
Noté: Theme 4 Quiz 5
Noté: Theme 4 Quiz 6
Noté: Theme 4 Quiz 7
Noté: Theme 4 Quiz 8
Noté: Theme 4 Quiz 9
Noté: Theme 4 Quiz 10
FAQ
Comment cela fonctionne
Coursework
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Créateurs
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.
Notation et examens
Great concise walk-through of neuro-imaging techniques. Low quality audio and a lot of background noise though.
Student presenters are not as good as professors.
Should have more practical work
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AJ
Great course. Learned quite a lot from the course. Only problem was the difficulty at first with the software and libraries stubbornly refusing to get setup. But, after realizing there was a VM provided with all intended software installed, everything was smooth sailing from there.