nipype.interfaces.dipy.simulate module

SimulateMultiTensor

Link to code

Bases: DipyBaseInterface

Interface to MultiTensor model simulator in dipy http://nipy.org/dipy/examples_built/simulate_multi_tensor.html

Example

>>> import nipype.interfaces.dipy as dipy
>>> sim = dipy.SimulateMultiTensor()
>>> sim.inputs.in_dirs = ['fdir00.nii', 'fdir01.nii']
>>> sim.inputs.in_frac = ['ffra00.nii', 'ffra01.nii']
>>> sim.inputs.in_vfms = ['tpm_00.nii.gz', 'tpm_01.nii.gz',
...                       'tpm_02.nii.gz']
>>> sim.inputs.baseline = 'b0.nii'
>>> sim.inputs.in_bvec = 'bvecs'
>>> sim.inputs.in_bval = 'bvals'
>>> sim.run()                                   
baselinea pathlike object or string representing an existing file

Baseline T2 signal.

in_dirsa list of items which are a pathlike object or string representing an existing file

List of fibers (principal directions).

in_fraca list of items which are a pathlike object or string representing an existing file

Volume fraction of each fiber.

in_vfmsa list of items which are a pathlike object or string representing an existing file

Volume fractions of isotropic compartiments.

bvaluesa list of items which are an integer

List of b-values (when table is automatically generated). (Nipype default value: [1000, 3000])

diff_isoa list of items which are a float

Diffusivity of isotropic compartments. (Nipype default value: [0.003, 0.00096, 0.00068])

diff_sfa tuple of the form: (a float, a float, a float)

Single fiber tensor. (Nipype default value: (0.0017, 0.0002, 0.0002))

gradientsa pathlike object or string representing an existing file

Gradients file.

in_bvala pathlike object or string representing an existing file

Input bvals file.

in_bveca pathlike object or string representing an existing file

Input bvecs file.

in_maska pathlike object or string representing an existing file

Mask to simulate data.

n_procan integer

Number of processes. (Nipype default value: 0)

num_dirsan integer

Number of gradient directions (when table is automatically generated). (Nipype default value: 32)

out_bvala pathlike object or string representing a file

Simulated b values. (Nipype default value: bval.sim)

out_bveca pathlike object or string representing a file

Simulated b vectors. (Nipype default value: bvec.sim)

out_filea pathlike object or string representing a file

Output file with fractions to be simluated. (Nipype default value: sim_dwi.nii.gz)

out_maska pathlike object or string representing a file

File with the mask simulated. (Nipype default value: sim_msk.nii.gz)

snran integer

Signal-to-noise ratio (dB). (Nipype default value: 0)

out_bvala pathlike object or string representing an existing file

Simulated b values.

out_bveca pathlike object or string representing an existing file

Simulated b vectors.

out_filea pathlike object or string representing an existing file

Simulated DWIs.

out_maska pathlike object or string representing an existing file

Mask file.