dangom
commented
5 years ago I don't know if this is a correct start. It's a partial translation of this matlab code, which is discussed at the ANTs main repo, into python. It's missing a final RAS to LPS conversion, so there may be some sign flips. It also adds in a dependency on transforms3d, which may potentially be undesirable.
def ants_to_human(aff, fixed):
"""Convert an ATNs affine_3x3 and a fixed center of rotation into a 4x4
affine matrix.
"""
mat = np.hstack((np.reshape(aff[:9], (3, 3)).T, aff[9:]))
m_translation = mat[:, 3]
mat = np.vstack((mat, [0, 0, 0, 1]))
m_offset = np.zeros((3,))
for i in range(3):
m_offset[i] = m_translation[i] + fixed[i]
for j in range(3):
m_offset[i] -= mat[i, j] * fixed[j]
mat[:3, 3] = m_offset
mat = np.linalg.inv(mat)
return mat
def human_to_more_human(mat):
"""Return translation and rotation parameter estimates from 4x4 affine matrix.
"""
tra, mrot, zoom, shear = transforms3d.affines.decompose44(mat)
rx = np.arctan2(mrot[1, 2], mrot[2, 2])
ry = np.arctan2(-mrot[2, 0], np.sqrt(mrot[2, 1] ** 2 + mrot[2, 2] ** 2))
rz = np.arctan2(mrot[1, 0], mrot[0, 0])
rot = np.array((rx, ry, rz))
return np.hstack((tra, rot))But a throw-away example shows that the estimated FD does not match what is currently implemented (but magnitudes are in the same ballpark).
from scipy.io import loadmat
affines = [loadmat(x[0])['AffineTransform_float_3_3'] for x in data_mcf['motion_parameters']]
fix = [loadmat(x[0])['fixed'].squeeze() for x in data_mcf['motion_parameters']]
mpars = np.vstack([human_to_more_human(ants_to_human(a, f)) for (a, f) in zip(affines, fix)])
fd_est = np.sum(np.abs(np.diff(mpars, axis=0)), axis=1)
plt.scatter(data_mcf['FD'], np.insert(fd_est, 0, 0, axis=0))
stnava
wangyibin0011
Is your feature request related to a problem? Please describe. Currently,
ants.motion_correctionoutputsmotion_parametersas a list of MAT files that are saved to a temporary folder. This makes it so that if the user wants to save these transformations (to my understanding), he has to move these outputs somewhere else, manually, and write a mapping.txt file that specifies which file belongs to each volume, given that names are random. It's also cumbersome to extract common motion parameter regressors from these MAT files from within python. My knowledge is that this requires calling in scipy or hdf5 to load the MAT files, extracting the affine from the dict, parsing it and storing the translation and rotation parameters manually. This also means that the end user has to know what the ANTs internal representation of an affine transformation looks like, which is well documented, but outside of ANTsPy.Describe the solution you'd like
have the user be able to specify where to save the transformation matrices, and have their filenames sorted by index. This would ease storing files and allow easy identification of which affine belongs to which volume. If the folder already contains files with the same name, either throw an error before starting the motion correction, have a parameter to toggle overwrite (could default to True I guess), or add a suffix (the FSL solution).
output an extra
motion_parameter_estimatesnp.array or dictionary containing translation and rotation estimates for better interop with other software packages.Describe alternatives you've considered Open to suggestions.