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ENH: Implement Jacobian weighting during unwarp [backport gh-391] #397

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ENH: Implement Jacobian weighting during unwarp [backport gh-391] #397

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7 changes: 5 additions & 2 deletions sdcflows/transform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,10 @@ def apply(
# fmap * ro_time is the voxel-shift map (VSM)
# The VSM is just the displacements field given in index coordinates
# voxcoords is the deformation field, i.e., the target position of each voxel
voxcoords[pe_axis, ...] += fmap.reshape(-1) * ro_time
vsm = fmap * ro_time
voxcoords[pe_axis, ...] += vsm.reshape(-1)

jacobian = 1 + np.gradient(vsm, axis=pe_axis)

# Prepare data
data = np.squeeze(np.asanyarray(spatialimage.dataobj))
Expand All @@ -212,7 +215,7 @@ def apply(
mode=mode,
cval=cval,
prefilter=prefilter,
).reshape(spatialimage.shape)
).reshape(spatialimage.shape) * jacobian

moved = spatialimage.__class__(
resampled, spatialimage.affine, spatialimage.header
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