brainweb_phantom

brainweb_phantom#

mrtwin.brainweb_phantom(ndim, subject, shape=None, model='single-pool', segtype='crisp', output_res=None, B0=1.5, cache=True, cache_dir=None, brainweb_dir=None, force=False, verify=True)[source]#

Get BrainWeb phantom.

Parameters:

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

  • subject (int) – Subject id to download.

  • shape (int | Sequence[int] | None, optional) – Shape of the output data, the data will be interpolated to the given shape. If int, assume isotropic matrix. The default is None (original shape).

  • 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 ("fuzzy" or "crisp") select fuzzy and crisp segmentation, respectively. If it is False, return a dense numeric phantom. The default is crisp.

  • output_res (float | Sequence[float] | None, optional) – Resolution of the output data, the data will be rescaled to the given resolution. If scalar, assume isotropic resolution. The default is None (estimate from shape assuming same fov).

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

  • cache (bool, optional) – If True, cache the phantom. The default is True.

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

  • brainweb_dir (CacheDirType, optional) – Brainweb_directory for brainweb segmentation caching. The default is None (~/.cache/brainweb).

  • force (bool, optional) – Force download even if the file already exists. The default is False.

  • verify (bool, optional) – Enable SSL verification. DO NOT DISABLE (i.e., verify=False) IN PRODUCTION. The default is True.

Returns:

Brainweb phantom.

Return type:

PhantomType

Examples

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

We can generate a dense single slice 2D phantom with a matrix size of (200, 200) at 1.085 mm isotropic resolution for the brainweb subject n=4 as:

>>> phantom = brainweb_phantom(ndim=2, subject=4, 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.brainweb_phantom#

Brainweb Phantom

Brainweb Phantom
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