CS-MRI-Recon

Description

This project was done as a part of EE5180 Machine Learning Course(Spring 2021) at IITM.

Perform Compressed Sensing Reconstruction and comparing outputs with state of the art.

OS Requirements

The code works on Ubuntu 20.04.1 and Windows 10 (BART was tried on Ubuntu 20.04.1)

Setup and python dependencies

apt-get update
apt-get install python3.6     # --> or any other system-specific command for installing python3 on your system.
pip install jupyter
pip install numpy
pip install matplotlib
pip install sigpy
pip install h5py
pip install scikit-image
pip install runstats
pip install pytorch_msssim
pip install pytorch-lightning==0.7.5
pip install test-tube
pip install Pillow

Clone from parent repo.
for utility functions

Dataset

all files: https://drive.google.com/drive/folders/14mrihZkUoasr1a4RGqqZ0jcVIkcYNEwr?usp=sharing

Download the .nii file from https://drive.google.com/file/d/1qQPLU0bu08WvK0bCoL6gIqzCJSPyYB9N/view?usp=sharing as input for all reconstructions

Running Files

Place any file in the root folder of the cloned repo and execute

References

https://arxiv.org/abs/2007.02471 https://arxiv.org/abs/1810.03982 https://dmitryulyanov.github.io/deep_image_prior https://github.com/facebookresearch/fastMRI/tree/master/fastmri_examples/cs