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3D volumetric medical image analysis without OpenCV.

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Name		Name	Last commit message	Last commit date
Latest commit History 61 Commits
lab1		lab1
lab2		lab2
lab3		lab3
lab4		lab4
lab_bonus		lab_bonus
lab_final		lab_final
notebooks		notebooks
.gitattributes		.gitattributes
.gitignore		.gitignore
Guide to Medical Image Analysis - Methods and Algorithms.pdf		Guide to Medical Image Analysis - Methods and Algorithms.pdf
LICENSE		LICENSE
README.md		README.md
main.py		main.py
requirements.txt		requirements.txt

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3D Medical Image Analysis Practice

Table of Contents

lab1 - interactive brain viewer and MRI modalities, FFT
lab2 - affine transform, image registration and application
lab3 - functional localization using bold fMRI
lab4 - image enhancement and segmentation
final - visual cortex decoding (mind reading using bold fMRI)
bonus - 3D surface reconstruction in Unity (marching cubes)

Libraries

numpy - https://github.com/Kyubyong/numpy_exercises
numpy - https://github.com/rougier/numpy-100
matplotlib - https://github.com/rougier/matplotlib-tutorial
matplotlib - https://matplotlib.org/tutorials/index.html
seaborn - https://seaborn.pydata.org/tutorial.html
Nilearn - https://nilearn.github.io/

Reference

MRI crash course at Albert Einstein College of Medicine - Youtube video series
FSL - https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
AFNI Academy - https://www.youtube.com/channel/UC40RiNZN7_dCuB6Lg7HJl1g/
AFNI Training Bootcamp - https://cbmm.mit.edu/afni
Andy's brain blog - https://www.youtube.com/c/AndrewJahn/playlists
HIPR2 - https://homepages.inf.ed.ac.uk/rbf/HIPR2/index.htm