Model-driven motion correction for medical imaging
Documentation: https://openmiblab.github.io/mdreg
Source code: https://github.com/openmiblab/mdreg
Installation
pip install mdregTypical usage
import mdreg
# Get some test data (variable flip angle MRI)
data = mdreg.fetch('VFA')
# Configure the signal model fit
fit_image = {
'func': mdreg.fit_spgr_vfa_lin, # VFA signal model
'FA': data['FA'], # Flip angle in degress
'progress_bar': True, # Show a progress bar
}
# Configure the coregistration method
fit_coreg = {
'package': 'elastix',
'spacing': data['spacing'],
}
# Perform the motion correction
coreg, defo, fit, pars = mdreg.fit(
data['array'], # Signal data to correct
fit_image = fit_image, # Signal model fit
fit_coreg = fit_coreg, # Coregistration
verbose = 2, # Show progress update
)
# Visualize the results
anim = mdreg.plot.animation(
coreg,
title = 'Motion corrected VFA',
'interval' : 500, # Time between animation frames in ms
'vmin' : 0, # Minimum value of the colorbar
'vmax' : np.percentile(coreg, 99), # Maximum value of the colorbar
)
License
Released under the Apache 2.0 license:
Copyright (C) 2023-2024 dcmri developers
2 maintainers
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