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FIX: Coerce MGHImages to Nifti1Images when plotting #769

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merged 4 commits into from
Jan 13, 2023
Merged

FIX: Coerce MGHImages to Nifti1Images when plotting #769

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c3b2c0f
FIX: Ensure anat image is Nifti
mgxd Jan 11, 2023
9ed9562
FIX: Ensure contour is also nii
mgxd Jan 11, 2023
0b3a6ae
Update niworkflows/viz/utils.py
mgxd Jan 11, 2023
5bf26e5
Update niworkflows/viz/utils.py
mgxd Jan 11, 2023
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6 changes: 6 additions & 0 deletions niworkflows/viz/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -341,11 +341,17 @@ def plot_registration(
if cuts is None:
raise NotImplementedError # TODO

# nilearn 0.10.0 uses Nifti-specific methods
anat_nii = nb.Nifti1Image.from_image(anat_nii)

out_files = []
if estimate_brightness:
plot_params = robust_set_limits(anat_nii.get_fdata().reshape(-1), plot_params)

# FreeSurfer ribbon.mgz
if contour:
contour = nb.Nifti1Image.from_image(anat_nii)

ribbon = contour is not None and np.array_equal(
np.unique(contour.get_fdata()), [0, 2, 3, 41, 42]
)
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