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; T2’ acts where a voxel holds several isochromats. Fat precesses at pypulseqpp’s fat shift, and every isochromat 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

count

Return how many isochromats isochromats() samples the brain as, with the same arguments.

isochromats

Return the brain sampled as isochromats, for simulate().

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.

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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