shepplogan_phantom

shepplogan_phantom#

mrtwin.shepplogan_phantom(ndim, shape, model='single-pool', segtype='crisp', B0=1.5, cache=None, cache_dir=None)[source]#

Get SheppLogan phantom.

Parameters:

  • ndim (int) – Number of spatial dimensions. If ndim == 2, use a single slice (central axial slice).

  • shape (int | Sequence[int]) – Shape of the output data. If int, assume isotropic matrix.

  • model (str, optional) –

    String selecting one of the built-in tissue models. Valid entries are:

    • "single-pool": Single pool tissue model.

    • "mw-model": Myelin Water (MW) + Free Water (Intra-Extracellular, IEW)

    • "mt-model": Macromolecular pool + Free Water (IEW + MW)

    • "mwmt-model": Macromolecular pool + MW + IEW

    The default is "single-pool".

  • segtype (str | bool, optional) – Phantom type. If it is a string ("crisp") select crisp segmentation. If it is False, return a dense numeric phantom. The default is crisp.

  • B0 (float, optional) – Static field strength in [T]. The default is 1.5.

  • cache (bool | None, optional) – If True, cache the phantom. The default is True for 3D phantoms and False for single-slice 2D.

  • cache_dir (CacheDirType, optional) – cache_directory for phantom caching. The default is None (~/.cache/mrtwin).

Returns:

Shepp-Logan phantom.

Return type:

PhantomType

Examples

>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> from mrtwin import shepplogan_phantom

We can generate a dense single slice 2D phantom with a matrix size of (200, 200) as:

>>> phantom = shepplogan_phantom(ndim=2, shape=200, segtype=False)

Phantom T1 and T2 maps, can be accessed as:

>>> fig, ax = plt.subplots(2, 1)

>>> im1 = ax[0].imshow(phantom.T1, cmap="magma", vmax=1500)
>>> ax[0].axis("off"), ax[0].set_title("T1 [ms]")
>>> fig.colorbar(im1, ax=ax[0], fraction=0.046, pad=0.04)

>>> im2 = ax[1].imshow(phantom.T2, cmap="viridis", vmax=150)
>>> ax[1].axis("off"), ax[1].set_title("T2 [ms]")
>>> fig.colorbar(im, ax=ax[1], fraction=0.046, pad=0.04)

Examples using mrtwin.shepplogan_phantom#

Shepp-Logan Phantom

Shepp-Logan Phantom

Static Field Simulation

Static Field Simulation

Transmit Field Simulation

Transmit Field Simulation
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