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cornucopia.kspace

ArrayCoilTransform 

ArrayCoilTransform(ncoils=8, fwhm=0.5, diameter=0.8, jitter=0.01, unit='fov', shape=4, sos=True, *, shared=True, **kwargs)

Bases: NonFinalTransform

Generate and apply random coil sensitivities (real or complex)

Parameters:

Name Type Description Default
ncoils int

Number of complex receiver channels

 8
fwhm float

Width of each receiver profile

 0.5
diameter float

Diameter of the ellipsoid on wich receivers are centered

 0.8
jitter float

Amount of jitter off the ellipsoid

 0.01
unit (fov, vox)

Unit of fwhm, diameter, jitter

 'fov'
shape int

Number of control points for the underlying smooth component.

 4

Other Parameters:

Name Type Description
returns [list or dict of] {'input', 'sos', 'uncombined', 'sens', 'netsens'}

Default is 'uncombined'.

  • 'sos': Sum of square combined (magnitude) image
  • 'uncombined': Uncombined (complex) coil images
  • 'sens': Uncombined (complex) coil sensitivities
  • 'netsens': Net (magnitude) coil sensitivity
shared (channels, tensors, channels + tensors, '')

Whether to share the sensitivities across channels/tensors

SumOfSquaresTransform 

SumOfSquaresTransform(*, returns=None, append=False, prefix=True, include=None, exclude=None)

Bases: FinalTransform

Compute the sum-of-squares across coils/channels

IntraScanMotionTransform 

IntraScanMotionTransform(shots=4, axis=-1, freq=True, pattern='sequential', translations=0.1, rotations=15, sos=True, coils=None, *, shared='channels', **kwargs)

Bases: NonFinalTransform

Model intra-scan motion

Parameters:

Name Type Description Default
shots int

Number of acquisition shots. The object is in a different position in each shot.

 4
axis int

Axis along which shots are acquired (slice or phase-encode)

 -1
freq bool

Motion happens across a phase-encode direction, which means that the k-space is build from pieces with different object position. This typically happens in "3D" acquisitions. If False, motion happens along the slice direction ("2D" acquisition).

 True
pattern (sequential, random)

k-space (or slice) sampling pattern. This argument encodes the frequencies (or slices) that are acquired in each shot. The 'sequential' options assumes that frequencies are acquired in order. The 'random' option assumes that frequencies are randomly distributed across shots.

 'sequential'
translations Sampler or float

Sampler (or upper-bound) for random translations (in % of FOV)

 0.1
rotations Sampler or float

Sampler (or upper-bound) for random rotations (in deg)

 15
coils Transform

A transform that generates a set of complex sensitivity profiles

 None

Other Parameters:

Name Type Description
returns [list or dict of] {'input', 'sos', 'uncombined', 'sens', 'netsens', 'flow', 'matrix', 'pattern'}

Default is 'sos'

  • 'sos': Sum of square combined (magnitude) image (C, X, Y, Z)
  • 'uncombined': Uncombined (complex) coil images (K, X, Y, Z)
  • 'sens': Uncombined (complex) coil sensitivities (K, X, Y, Z)
  • 'netsens': Net (magnitude) coil sensitivity (1, X, Y, Z)
  • 'flow': Displacement field in each shot (N, 3, X, Y, Z)
  • 'matrix': Rigid matrix in each shot (N, 4, 4)
  • 'pattern': Frequencies acquired in each shot (N, X)
shared (channels, tensors, channels + tensors, '')

Whether to share the parameters across channels/tensors

FinalIntraScanMotionTransform 

FinalIntraScanMotionTransform(motion, patterns, sens=None, axis=-1, freq=False, **kwargs)

Bases: FinalTransform

Parameters:

Name Type Description Default
motion FinalTransform
required
patterns tensor
required
sens FinalTransform
None
axis int
-1

SmallIntraScanMotionTransform 

SmallIntraScanMotionTransform(translations=0.05, rotations=5, axis=-1, *, shared='channels', **kwargs)

Bases: IntraScanMotionTransform

Model intra-scan motion that happens once across k-space

Parameters:

Name Type Description Default
translations Sampler or float

Sampler (or upper-bound) for random translations (in % of FOV)

 0.05
rotations Sampler or float

Sampler (or upper-bound) for random rotations (in deg)

 5
axis int

Axis along which shots are acquired (slice or phase-encode)

 -1
shared (channels, tensors, channels + tensors, '')
'channels'