interfaces.dipy.simulate

SimulateMultiTensor

Link to code

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()                                   

Inputs:

[Mandatory]
baseline: (an existing file name)
        baseline T2 signal
in_dirs: (a list of items which are an existing file name)
        list of fibers (principal directions)
in_frac: (a list of items which are an existing file name)
        volume fraction of each fiber
in_vfms: (a list of items which are an existing file name)
        volume fractions of isotropic compartiments

[Optional]
bvalues: (a list of items which are an integer (int or long), nipype
         default value: [1000, 3000])
        list of b-values (when table is automatically generated)
diff_iso: (a list of items which are a float, nipype default value:
         [0.003, 0.00096, 0.00068])
        Diffusivity of isotropic compartments
diff_sf: (a tuple of the form: (a float, a float, a float), nipype
         default value: (0.0017, 0.0002, 0.0002))
        Single fiber tensor
gradients: (an existing file name)
        gradients file
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_bval: (an existing file name)
        input bvals file
in_bvec: (an existing file name)
        input bvecs file
in_mask: (an existing file name)
        mask to simulate data
n_proc: (an integer (int or long), nipype default value: 0)
        number of processes
num_dirs: (an integer (int or long), nipype default value: 32)
        number of gradient directions (when table is automatically
        generated)
out_bval: (a file name, nipype default value: bval.sim)
        simulated b values
out_bvec: (a file name, nipype default value: bvec.sim)
        simulated b vectors
out_file: (a file name, nipype default value: sim_dwi.nii.gz)
        output file with fractions to be simluated
out_mask: (a file name, nipype default value: sim_msk.nii.gz)
        file with the mask simulated
snr: (an integer (int or long), nipype default value: 0)
        signal-to-noise ratio (dB)

Outputs:

out_bval: (an existing file name)
        simulated b values
out_bvec: (an existing file name)
        simulated b vectors
out_file: (an existing file name)
        simulated DWIs
out_mask: (an existing file name)
        mask file