Course overview and schedule:
Syllabus
Tutorials:
Matlab tutorials: several courses from Mathworks,
and Open Course Work from MIT
Linear Algebra: Open Course Work from MIT
Digital Signal Processing: graphic demonstrations in matlab
Matlab tutorial from week 2: m-file, mri in .mat format, brain mask in .mat format
Short overview of geometric transforms.
Video series explaining
basics of NMR/MRI technology.
Lectures:
1. Introduction
2. X-ray Imaging
3. Intensity manipulations
4. Computed Tomography
5. 2D reconstruction from Projections
6. Nuclear Imaging
7. Maximum Likelihood Reconstruction
8. Nuclear Magnetic Resonance
9. Magnetic Resonance Imaging
10. Fourier Transform Review
11. Point Spread Function, Inverse Filtering,
Wiener Filtering, Sharpening, ...
12. Deep networks for image segmentation
Software:
Matlab toolbox for reading/writing MRI files: download (Unzip into your matlab path and use "load_untouch_nii.m" to load provided mri file)
Sample code for Keras: Jupyter notebook
Sample code and data for segmentation assignment google drive, zip file
Data:
CT image: head 1, head 2, mouse.
Fan beam projection: MicroCT of mouse femur
Head x-ray: head-xray1, head-xray2
MRI in .hdr/.img format: hdr, img
BME 310 segmentation exercise: data
Images for homework 1: blood1.tif, cell.tif, penny.mat.
Image for homework 4: homodimer_staining.tiff
