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()                                   # doctest: +SKIP
baseline : a pathlike object or string representing an existing file
Baseline T2 signal.
in_dirs : a list of items which are a pathlike object or string representing an existing file
List of fibers (principal directions).
in_frac : a list of items which are a pathlike object or string representing an existing file
Volume fraction of each fiber.
in_vfms : a list of items which are a pathlike object or string representing an existing file
Volume fractions of isotropic compartiments.
bvalues : a list of items which are an integer (int or long)
List of b-values (when table is automatically generated). (Nipype default value: [1000, 3000])
diff_iso : a list of items which are a float
Diffusivity of isotropic compartments. (Nipype default value: [0.003, 0.00096, 0.00068])
diff_sf : a tuple of the form: (a float, a float, a float)
Single fiber tensor. (Nipype default value: (0.0017, 0.0002, 0.0002))
gradients : a pathlike object or string representing an existing file
Gradients file.
in_bval : a pathlike object or string representing an existing file
Input bvals file.
in_bvec : a pathlike object or string representing an existing file
Input bvecs file.
in_mask : a pathlike object or string representing an existing file
Mask to simulate data.
n_proc : an integer (int or long)
Number of processes. (Nipype default value: 0)
num_dirs : an integer (int or long)
Number of gradient directions (when table is automatically generated). (Nipype default value: 32)
out_bval : a pathlike object or string representing a file
Simulated b values. (Nipype default value: bval.sim)
out_bvec : a pathlike object or string representing a file
Simulated b vectors. (Nipype default value: bvec.sim)
out_file : a pathlike object or string representing a file
Output file with fractions to be simluated. (Nipype default value: sim_dwi.nii.gz)
out_mask : a pathlike object or string representing a file
File with the mask simulated. (Nipype default value: sim_msk.nii.gz)
snr : an integer (int or long)
Signal-to-noise ratio (dB). (Nipype default value: 0)
out_bval : a pathlike object or string representing an existing file
Simulated b values.
out_bvec : a pathlike object or string representing an existing file
Simulated b vectors.
out_file : a pathlike object or string representing an existing file
Simulated DWIs.
out_mask : a pathlike object or string representing an existing file
Mask file.