This repository hosts jupyter notebooks for that cover basics of fMRI preprocessing and analyses.
Instructors: Jeremy Huckins & Alex daSilva
Website developed by: Jeremy Huckins & Jin Hyun Cheong
Prelab: Basic linux tutorial Please read and work through the main page and sections 1-5,7,14. Please see Jeremy or Alex if you need help getting to or installing a terminal on your laptop. If you don't have a laptop you can bring to class please let Jeremy know.
Lab 01: Navigating the terminal and viewing a brain using fsl/spm/afni.
In this lab we cover the basics of ssh logging into a cluster server and using a VNC environment. We learn about basic shell commands that can be used for navigating the terminal. We launch different fMRI analysis softwares, FSL, SPM, and AFNI, for interactive viewing of brain images.
Lab 04: Statistics and Visualization
[Lab 05: Other programs (in prep)]
Basic concept of fMRI & history
Explanation of k-space and image through FT
http://mriquestions.com/index.html
https://practicalfmri.blogspot.com/
Intro to MR physics with good figures
Explanation of MRI with good figures
Method 1: Graphical walk-through
Method 2: A docker container for 3D printing a brain As a note, Jin mentioned that before printing you may want to merge the hemispheres in MeshLab.