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fix: Remove checks for unit zooms and symmetric rotations in template warp #3376

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Merged
merged 2 commits into from
Oct 10, 2024
Merged

fix: Remove checks for unit zooms and symmetric rotations in template warp #3376

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23c4636
fix: Accept warps with isotropic spacing
effigies Oct 9, 2024
1607996
FIX: Drop safeguard errors; manually verified weird references
effigies Oct 10, 2024
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11 changes: 2 additions & 9 deletions fmriprep/utils/transforms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,8 @@ def load_ants_h5(filename: Path) -> nt.base.TransformBase:
# * Always return a nitransforms TransformBase
# * Construct warp affine from fixed parameters
#
# This should be upstreamed into nitransforms
# This has been upstreamed into nitransforms.
# Future versions should switch to using nitransforms directly.
h = h5py.File(filename)
xform = ITKCompositeH5.from_h5obj(h)

Expand Down Expand Up @@ -78,14 +79,6 @@ def load_ants_h5(filename: Path) -> nt.base.TransformBase:
spacing = transform2['TransformFixedParameters'][6:9]
direction = transform2['TransformFixedParameters'][9:].reshape((3, 3))

# We are not yet confident that we handle non-unit spacing
# or direction cosine ordering correctly.
# If we confirm or fix, we can remove these checks.
if not np.allclose(spacing, 1):
raise ValueError(f'Unexpected spacing: {spacing}')
if not np.allclose(direction, direction.T):
raise ValueError(f'Asymmetric direction matrix: {direction}')

# ITK uses LPS affines
lps_affine = compose_affine(T=origin, R=direction, Z=spacing)
ras_affine = np.diag([-1, -1, 1, 1]) @ lps_affine
Expand Down