GESeries.NiiBase

GESeries.NiiBase(nii, orientation=('L', 'P', 'S'))

Wraps a NIfTI image with orientation-aware loading, display, and I/O helpers.

Attributes¶

Name	Description
`affine`	The affine matrix of the NIfTI image.
`brain_mask`	The brain mask as a NiiBase, loaded if present else created on access.
`nii`
`nii_path`
`orientation`

Methods¶

Name	Description
apply_mask	Return the image data with voxels outside mask set to NaN.
display	Display the image, optionally masked, via plotting.images.display_images.
get_brain_mask	Find (or optionally create) the brain mask NIfTI next to this image.
images	Return the image data array, oriented per orientation or display_plane.
overlay_on_T1	Overlay this image on a T1 image, resampling and masking as needed.
resample_self_to	Return a new NiiBase with this image resampled onto target_nii’s grid.
save	Save the NIfTI image to output_path as a Nifti1Image.
with_new_data	Return a new NiiBase wrapping new_data, keeping this image’s header/affine.

apply_mask¶

GESeries.NiiBase.apply_mask(mask)

Return the image data with voxels outside mask set to NaN.

display¶

GESeries.NiiBase.display(
    orientation=None,
    display_plane=None,
    mask=None,
    **kwargs,
)

Display the image, optionally masked, via plotting.images.display_images.

Displays an interactive image-grid widget and returns nothing.

get_brain_mask¶

GESeries.NiiBase.get_brain_mask(
    create=False,
    mask_keyword='_bet.nii',
    **extract_kwargs,
)

Find (or optionally create) the brain mask NIfTI next to this image.

Looks for a brain mask NIfTI (matching mask_keyword) in the same folder as self.nii_path. If none is found and create is True, a mask is generated with HD-BET via :func:utils.images.extract_brain and loaded. The mask is returned as its own :class:NiiBase.

Parameters¶

Name	Type	Description	Default
create	bool	If True, run HD-BET brain extraction when no mask is found.	`False`
mask_keyword	str	Substring identifying the brain mask NIfTI file.	`'_bet.nii'`
**extract_kwargs		Forwarded to `utils.images.extract_brain`.	`{}`

Returns¶

Name	Type	Description
	NiiBase	The brain mask wrapped as a NiiBase.

Raises¶

Name	Type	Description
	ValueError	If this NIfTI was not loaded from a path (no folder to search).
	FileNotFoundError	If no mask is found and `create` is False.

images¶

GESeries.NiiBase.images(
    orientation=None,
    display_plane=None,
    caching=True,
    **kwargs,
)

Return the image data array, oriented per orientation or display_plane.

overlay_on_T1¶

GESeries.NiiBase.overlay_on_T1(
    t1,
    resample_kwargs=None,
    orientation=None,
    display_plane=None,
    mask=None,
    **kwargs,
)

Overlay this image on a T1 image, resampling and masking as needed.

resample_self_to¶

GESeries.NiiBase.resample_self_to(target_nii, **kwargs)

Return a new NiiBase with this image resampled onto target_nii’s grid.

save¶

GESeries.NiiBase.save(output_path)

Save the NIfTI image to output_path as a Nifti1Image.

with_new_data¶

GESeries.NiiBase.with_new_data(new_data, new_affine=None)

Return a new NiiBase wrapping new_data, keeping this image’s header/affine.