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Negida Research Academy/Neuroimaging analysis of MRI using MATLAB - Arabic
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Neuroimaging analysis of MRI using MATLAB - Arabic

  • Course
  • 41 Lessons

The first and only neuroimaging analysis course in Arabic, given by Dr. Ahmed Negida, explains a much-needed skill for neuroscience research, the basics, and the methods of analyzing MRI images. All lectures include practical applications using the existing online datasets.
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About the instructor

Ahmed Negida

MBBCh, PhD

Dr. Negida is a research scientist with diverse experience in clinical research and a focus on improving the treatment of neurological and neurosurgical diseases.

Education:
  • MBBCh from Zagazig University, Egypt
  • Ph.D. by Publication from the University of Portsmouth, UK

Research Fellowships:
  • Bahcesehir University (Turkey)
  • Harvard Medical School, MA (USA)
  • Virginia Commonwealth University, VA (USA)
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Course Announcemenet

Contents

Preparation information - Lecture 1

[JOIN NOW] Telegram Group of the Course
Course Timeline
Lecture 1: Basics of Neuroimaging Analysis
Recommended Requirements
MATLAB System Requirements
(OPTIONAL): Buying MATLAB
(WAIT) MATLAB - 30 day free trial
Download the SPM12
Assignment 1

Section 1: Introduction & Basics

Introduction to MATLAB graphical user interface
Basic MATLAB commands
Introduction to Neuroimaging with MRI
Factors Affecting Imaging Quality
File Formats
Converting DICOM to Nifti
Organizing MRI data

Section 2: Preprocessing of MRI

Introduction to preprocessing
Realignment and Motion Correction
Coregistration
Spatial Normalization
Smoothing
Summary of preprocessing
Introduction & preprocessing.mp4
Preprocessing on SPM 12 & Segmentation on CAT12.mp4
Discussion After VBM & Quality Checks.mp4

Analysis of Structural MRI images

Download CAT12 Toolbox
Download SPM Neuroanatomy Toolbox version 3.0 (JuBrain)
Terminal Codes to Bypass MacOS security
Lecture 2: Analysis of Voxel-based Morphometry
Lecture 3: Measurement of Cortical Thickness & More Practice on the VBM

Analysis of Functional MRI images

Download Conn Toolbox
Analysis of resting state fMRI - First Level Analysis
Analysis of resting-state fMRI - second level analysis (group analysis)
Lecture 4: Analysis of BOLD Signal - Part 1
Lecture 5: Analysis of BOLD Signal - Part 2
Case Study - Example for a complete fMRI analysis of a clinical trial

Additional Resources

Lecture 6: Revision and Q&A
Other Alternative (less powerful) Neuroimaging Analysis Software
MATLAB script to calculate the Grey Matter Density using the weighted sum method

FLAIR MRI analysis

Lesion Segmentation Tool
Counting the Number of WMHs and Total Lesion Volume