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deepmr.brainweb

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deepmr.brainweb#

deepmr.brainweb(idx, npix=None, nslices=1, B0=3.0, cache_dir=None)[source]#

Initialize a brain-shaped phantom for MR simulations.

This function generates a brain-shaped phantom [1-3] for qMR or MR simulations based on the provided parameters.

Parameters:

  • idx (int) – Brainweb ID (0 to 19).

  • npix (Iterable[int], optional) – In-plane matrix size. The default is None.

  • nslices (int, optional) – Number of slices. An isotropic [npix, npix, npix] phantom can be generated, for convenience, by setting nslices to -1. The default is 1.

  • B0 (float, optional) – Static field strength in [T]. The default is 3.0.

  • cache_dir (os.PathLike) – Directory to download the data.

Returns:

phantom – Dictionary of BrainWeb maps (M0, T1, T2, T2star, chi) of shape (nslices, ny, nx) (qmr == True). Units for T1, T2 and T2star are [ms]; for chi, units are [ppm].

Return type:

torch.Tensor, dict

Examples

>>> import deepmr

We can generate a single-slice BrainWeb phantom as:

>>> phantom = deepmr.brainweb(128)
>>> phantom.keys()
dict_keys(['M0', 'T1', 'T2', 'T2star', 'chi'])

Each map will have (nslices, npix, npix) shape:

>>> phantom["M0"].shape
torch.Size([128, 128])

We also support multiple slices:

>>> phantom = deepmr.brainweb(128, 32)
>>> phantom["M0"].shape
torch.Size([32, 128, 128])

Notes

The brainweb is set in the following order:

  • The cache_dir passed as argument.

  • The environment variable BRAINWEB_DIR.

  • The default cache__dir ~/brainweb.

References

[1] D.L. Collins, A.P. Zijdenbos, V. Kollokian, J.G. Sled, N.J. Kabani, C.J. Holmes, A.C. Evans,

Design and Construction of a Realistic Digital Brain Phantom, IEEE Transactions on Medical Imaging, vol.17, No.3, p.463–468, June 1998

[2] casperdcl/brainweb

[3] paquiteau/brainweb-dl

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