def compare_xforms(lta_list, norm_threshold=15):
"""
Computes a normalized displacement between two affine transforms as the
maximum overall displacement of the midpoints of the faces of a cube, when
each transform is applied to the cube.
This combines displacement resulting from scaling, translation and rotation.
Although the norm is in mm, in a scaling context, it is not necessarily
equivalent to that distance in translation.
We choose a default threshold of 15mm as a rough heuristic.
Normalized displacement above 20mm showed clear signs of distortion, while
"good" BBR refinements were frequently below 10mm displaced from the rigid
transform.
The 10-20mm range was more ambiguous, and 15mm chosen as a compromise.
This is open to revisiting in either direction.
See discussion in
`GitHub issue #681`_ <https://github.com/poldracklab/fmriprep/issues/681>`_
and the `underlying implementation
<https://github.com/nipy/nipype/blob/56b7c81eedeeae884ba47c80096a5f66bd9f8116/nipype/algorithms/rapidart.py#L108-L159>`_.
Parameters
----------
lta_list : list or tuple of str
the two given affines in LTA format
norm_threshold : float (default: 15)
the upper bound limit to the normalized displacement caused by the
second transform relative to the first
"""
from fmriprep.interfaces.surf import load_transform
from nipype.algorithms.rapidart import _calc_norm_affine
bbr_affine = load_transform(lta_list[0])
fallback_affine = load_transform(lta_list[1])
norm, _ = _calc_norm_affine([fallback_affine, bbr_affine],
use_differences=True)
return norm[1] > norm_threshold
def compare_xforms(lta_list, norm_threshold=15):
"""
Computes a normalized displacement between two affine transforms as the
maximum overall displacement of the midpoints of the faces of a cube, when
each transform is applied to the cube.
This combines displacement resulting from scaling, translation and rotation.
Although the norm is in mm, in a scaling context, it is not necessarily
equivalent to that distance in translation.
We choose a default threshold of 15mm as a rough heuristic.
Normalized displacement above 20mm showed clear signs of distortion, while
"good" BBR refinements were frequently below 10mm displaced from the rigid
transform.
The 10-20mm range was more ambiguous, and 15mm chosen as a compromise.
This is open to revisiting in either direction.
See discussion in
`GitHub issue #681`_ <https://github.com/poldracklab/fmriprep/issues/681>`_
and the `underlying implementation
<https://github.com/nipy/nipype/blob/56b7c81eedeeae884ba47c80096a5f66bd9f8116/nipype/algorithms/rapidart.py#L108-L159>`_.
Parameters
----------
lta_list : list or tuple of str
the two given affines in LTA format
norm_threshold : float (default: 15)
the upper bound limit to the normalized displacement caused by the
second transform relative to the first
"""
from fmriprep.interfaces.surf import load_transform
from nipype.algorithms.rapidart import _calc_norm_affine
bbr_affine = load_transform(lta_list[0])
fallback_affine = load_transform(lta_list[1])
norm, _ = _calc_norm_affine([fallback_affine, bbr_affine], use_differences=True)
return norm[1] > norm_threshold