osf_phantom

osf_phantom#

mrtwin.osf_phantom(ndim, subject, shape=None, output_res=None, B0=3.0, cache=True, cache_dir=None, osf_dir=None, force=False, verify=True)[source]#

Get OSF 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).

  • output_res (float | Sequence[float] | None, optional) – Resolution of the output data, the data will be rescale 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 3.0.

  • 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).

  • osf_dir (CacheDirType, optional) – osf_directory for brainweb segmentation caching. The default is None (~/.cache/osf).

  • 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:

OSF phantom.

Return type:

PhantomType

Examples

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

We can generate a dense single slice 2D phantom with a matrix size of (256, 256) at 1.0625 mm isotropic resolution for the OSF subject n=1 as:

>>> phantom = osf_phantom(ndim=2, subject=1)

Phantom T1 and T2 maps, can be accessed as:

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

>>> im1 = ax[0].imshow(phantom.T1, cmap="magma", vmin=0, vmax=3500)
>>> 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", vmin=0, vmax=250)
>>> 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.osf_phantom#

Open Science CBS Neuroimaging Repository Phantom

Open Science CBS Neuroimaging Repository Phantom
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