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()
Mandatory Inputs:

  • 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.

Optional Inputs:

  • bvalues (a list of items which are an integer) – 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) – Number of processes. (Nipype default value: 0)

  • num_dirs (an integer) – 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) – Signal-to-noise ratio (dB). (Nipype default value: 0)

Outputs:

  • 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.