nipype.interfaces.dipy.simulate module¶
SimulateMultiTensor¶
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.