BrainWeb

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BrainWeb#

class pulserver.virtual.BrainWeb[source]#

Bases: object

BrainWeb’s normal brain, received by one coil or several.

The fuzzy tissue model of BrainWeb’s normal brain (Collins et al., IEEE Trans Med Imaging 17:463, 1998) gives each 1 mm voxel the fraction of it each tissue class fills. brainweb-dl downloads it on first use into its cache, which the brainweb extra installs. The brain lies as a subject lying head first and supine, with the origin of its MNI coordinates, the anterior commissure, at the isocentre: the physical x axis points to the subject’s left, y posterior and z superior. Each tissue class relaxes with the T1, T2 and T2’ relaxation() derives at the field it is scanned at from the parameters BrainWeb’s simulator gives it at 1.5 T (Kwan et al., IEEE Trans Med Imaging 18:1085, 1999), and has the proton density the simulator gives it. Fat precesses at pypulseqpp’s fat shift, and every voxel at the field field_ppm its head adds. The coils are those of Phantom, fixed in the physical frame.

Parameters:

  • coils – Receive channels.

  • period – Spatial period of the sensitivities, in metres.

  • depth – Their modulation depth.

  • directory – brainweb-dl’s cache; BRAINWEB_DIR, or ~/.cache/brainweb, without one.

  • susceptibility – Whether the field the head’s susceptibility adds acts on it.

  • t2_prime – T2’, in s, by tissue class, in place of the one relaxation() derives, at any field.

  • diffusion – Isotropic diffusion coefficient, in m²/s, by tissue class, as DIFFUSION gives them; a class without one does not diffuse.

Methods

proton_density

Return the proton density of a slab thickness thick along normal at each of (n, 3) physical points, in metres.

relaxation

Return the T1, T2 and T2', in s, of each tissue class at field_t T.

tissue

Return the brain sampled for the Fourier engine: each tissue of each cube spacing wide, at the cube's centre.

Attributes

DIFFUSION

Isotropic diffusion coefficients, in m²/s, of the tissue classes whose water diffusion is measured: the apparent diffusion coefficients of cortical grey matter and of white matter in adults (Helenius et al., AJNR Am J Neuroradiol 23:194, 2002), which glial matter and connective tissue take as BrainWeb gives them those tissues' relaxation, and that of free water at 37 degrees C for CSF (Holz et al., Phys Chem Chem Phys 2:4740, 2000).

field_ppm

The field the head adds to B0 at each voxel, (z, y, x), in ppm of B0, as a first-order shim leaves it.

fractions

The fraction of each voxel each tissue fills, (z, y, x, tissue), downloaded on first use.
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