utils.nifti - MNUtils

utils.nifti

Functions¶

Name	Description
apply_half_voxel_shift	Shift an affine by half a voxel in x/y (and optionally z). Deprecated, always raises.
get_display_affine	Return the affine mapping display voxel indices (after orient_nifti) to world mm.
get_display_zooms	Return the (row, col) physical voxel edge lengths of the displayed grid, in mm.
orient_nifti	Reorient and rotate a NIfTI image’s data array for display.
resample_and_orient_nifti	Resample `source_nii` onto `target_nii`’s grid, then orient both for display.
resample_nifti	Resample `source_nii` into `target_nii`’s voxel grid via `nibabel.processing`.

apply_half_voxel_shift¶

utils.nifti.apply_half_voxel_shift(affine, shift_z_axis=False)

Shift an affine by half a voxel in x/y (and optionally z). Deprecated, always raises.

Parameters¶

Name	Type	Description	Default
affine	ndarray	The affine to shift.	required
shift_z_axis	bool	Whether to also shift the z axis. Defaults to False.	`False`

Returns¶

Name	Type	Description
	ndarray	The shifted affine. Unreachable, since this function always raises.

Raises¶

Name	Type	Description
	DeprecationWarning	Always. Half voxel shifts are usually a symptom of a bad affine definition; use dcm2nii to convert DICOMs and use its affine instead.

get_display_affine¶

utils.nifti.get_display_affine(nii, orientation=None, display_plane=None)

Return the affine mapping display voxel indices (after orient_nifti) to world mm.

orient_nifti applies apply_orientation then flipud(rot90(k=1)) which equals a transpose of axes 0 and 1. This function encodes both steps as an affine. Use inv(get_display_affine(t1)) @ mrsi_affine to get mrsi→display mapping.

Parameters¶

Name	Type	Description	Default
nii	nibabel.spatialimages.SpatialImage or GESeries.NiiBase	The image to compute the display affine for.	required
orientation	tuple[str, str, str]	Target axis codes. Defaults to `rcParams["nifti.orientation"]` if neither this nor `display_plane` is given.	`None`
display_plane	('axial', 'coronal', 'sagittal')	If given, overrides `orientation` with a preset for the named plane, matching `orient_nifti`.	`"axial"`

get_display_zooms¶

utils.nifti.get_display_zooms(nii, orientation=None, display_plane=None)

Return the (row, col) physical voxel edge lengths of the displayed grid, in mm.

The column norms of get_display_affine’s first two columns give the physical spacing along the two in-plane axes orient_nifti puts at positions 0 and 1 -- correct even for oblique/rotated affines, unlike reading nii.header.get_zooms() and guessing which entries survived the reorientation/transpose. Meant to be passed straight through as display_images(..., zooms=...).

orient_nifti¶

utils.nifti.orient_nifti(
    nii,
    orientation=None,
    display_plane=None,
    caching=True,
)

Reorient and rotate a NIfTI image’s data array for display.

Applies the requested axis orientation (or one derived from display_plane), then transposes axes 0 and 1 to match the display convention used elsewhere in this module.

Parameters¶

Name	Type	Description	Default
nii	spatialimages.SpatialImage or GESeries.NiiBase	The image to orient.	required
orientation	tuple[str, str, str]	Target axis codes. Defaults to `rcParams["nifti.orientation"]` if neither this nor `display_plane` is given.	`None`
display_plane	('axial', 'coronal', 'sagittal')	If given, overrides `orientation` with a preset for the named plane.	`"axial"`
caching	bool	Whether to cache the underlying image data (more memory, faster repeat access) or not (less memory, slower repeat access). Defaults to True.	`True`

Returns¶

Name	Type	Description
	ndarray	The reoriented image data array.

resample_and_orient_nifti¶

utils.nifti.resample_and_orient_nifti(
    source_nii,
    target_nii,
    orientation=None,
    display_plane=None,
    **kwargs,
)

Resample source_nii onto target_nii’s grid, then orient both for display.

Parameters¶

Name	Type	Description	Default
source_nii	spatialimages.SpatialImage or GESeries.NiiBase	The image to resample.	required
target_nii	spatialimages.SpatialImage or GESeries.NiiBase	The image whose grid to resample onto.	required
orientation	tuple[str, str, str]	Target axis codes passed to `orient_nifti`. Defaults to `rcParams["nifti.orientation"]`.	`None`
display_plane	('axial', 'coronal', 'sagittal')	If given, overrides `orientation` with a preset for the named plane.	`"axial"`
**kwargs	Any	Additional keyword arguments passed to `resample_nifti`.	`{}`

Returns¶

Name	Type	Description
	tuple[ndarray, ndarray]	The oriented target image data and the oriented resampled data.

resample_nifti¶

utils.nifti.resample_nifti(source_nii, target_nii, **kwargs)

Resample source_nii into target_nii’s voxel grid via nibabel.processing.

Parameters¶

Name	Type	Description	Default
source_nii	spatialimages.SpatialImage or GESeries.NiiBase	The image to resample.	required
target_nii	spatialimages.SpatialImage or GESeries.NiiBase	The image whose grid to resample onto.	required
**kwargs	Any	Overrides for the `nifti.resample.*` rcParams, passed to `nibabel.processing.resample_from_to`.	`{}`

Returns¶

Name	Type	Description
	spatialimages.SpatialImage	The resampled image.