3D Variable Flip Angle (non-linear)

This example illustrates motion correction of a 3D time series with variable flip angles (VFA). The motion correction is performed with 3D coregistration and a non-linear signal model fit.

Import packages and load data

import numpy as np
import mdreg

# Example data included in mdreg
data = mdreg.fetch('VFA')

# Variables used in this examples
array = data['array']       # 4D signal data (x, y, z, FA)
FA = data['FA']             # The FA values in degrees
spacing = data['spacing']   # (x,y,z) voxel size in mm.

Signal model

The signal data are acquired using a spoiled gradient-echo sequence in the steady-state, with different flip angles:

\(S(\phi)=S_0\sin{\phi} \frac{1-e^{-T_R/T_1}}{1-\cos{\phi}\,e^{-T_R/T_1}}\)

Here \(S(\phi)\) is the signal at flip angle \(\phi\), \(S_0\) a scaling factor, \(T_R\) the repetition time and \(T_1\) the longitudinal relaxation time.

Defining the following constant in the range [0,1]:

\(E=e^{-T_R/T_1}\)

The signal model can be written as:

\(S(\phi) = S_0\sin{\phi} \frac{1-E}{1-\cos{\phi}\,E}\)

Perform motion correction

The signal model above is included in mdreg as the function mdreg.spgr_vfa_nonlin, which requires the flip angle (FA) in degrees as input:

vfa_fit = {
    'func': mdreg.spgr_vfa_nonlin,      # VFA signal model
    'FA': FA,                           # Flip angle in degress
}

For this example we will use a coarse deformation field with grid spacing 50mm:

coreg_params = {
    'spacing': spacing,
    'FinalGridSpacingInPhysicalUnits': 50.0,
}

We can now perform the motion correction:

coreg, defo, fit, pars = mdreg.fit(
    array,                          # Signal data to correct
    fit_image = vfa_fit,            # Signal model
    fit_coreg = coreg_params,       # Coregistration model
    maxit = 2,                      # Maximum number of iterations
)

Visualize the results

We visualise the original data and results of the computation using the builtin mdreg.animation function. Since we want to call this 3 times, we define the settings up front:

plot_settings = {
    'interval' : 500,                   # Time between animation frames in ms
    'vmin' : 0,                         # Minimum value of the colorbar
    'vmax' : np.percentile(array,99),   # Maximum value of the colorbar
    'show' : True,                      # Display the animation on screen
}

Now we can plot the data, coregistered images and model fits separately:

anim = mdreg.animation(array, title='Original data', **plot_settings)

Once Loop Reflect

anim = mdreg.animation(coreg, title='Motion corrected', **plot_settings)

Once Loop Reflect

anim = mdreg.animation(fit, title='Model fit', **plot_settings)

Once Loop Reflect

It’s also instructive to show the deformation field and check whether deformations are consistent with the effect of breathing motion. Since the deformation field is a vector we show here its norm:

# Get the norm of the deformation field and adjust the plot settings
defo = mdreg.defo_norm(defo)
plot_settings['vmax'] = np.percentile(defo, 99)

# Display the norm of the deformation field
anim = mdreg.animation(defo, title='Deformation field', **plot_settings)
#
#

Once Loop Reflect