Dynamic lung water magnetic resonance imaging during exercise stress

This code is for the manuscript (in sub): Seemann, F., et al. Dynamic lung water magnetic resonance imaging during exercise stress

This repository contains

Matlab pipeline code for inline reconstruction and analysis
Python processing for lung segmentation for analysis
Image registration package

NHLBI TOOLBOX GADGETRON Installation

Repository with gadgetron image reconstruction code: https://github.com/NHLBI-MR/selfgated_noncartesian_reconstruction.git

% GADGETRON MATLAB

Install application through matlab
https://www.mathworks.com/matlabcentral/fileexchange/72715-gadgetron
Make directory "+nhlbi" inside the +gadgetron class

Requires python packages

numpy
matplotlib
torch
torchvision
scipy

pip install numpy matplotlib torch torchvision scipy the trained neural network is named best_lung_seg_model.pkl and is saved in the python folder