nipype.interfaces.dipy.tensors module

DTI

Link to code

Bases: DipyDiffusionInterface

Calculates the diffusion tensor model parameters

Example

>>> import nipype.interfaces.dipy as dipy
>>> dti = dipy.DTI()
>>> dti.inputs.in_file = 'diffusion.nii'
>>> dti.inputs.in_bvec = 'bvecs'
>>> dti.inputs.in_bval = 'bvals'
>>> dti.run()                                   # doctest: +SKIP
in_bval : a pathlike object or string representing an existing file
Input b-values table.
in_bvec : a pathlike object or string representing an existing file
Input b-vectors table.
in_file : a pathlike object or string representing an existing file
Input diffusion data.
b0_thres : an integer (int or long)
B0 threshold. (Nipype default value: 700)
mask_file : a pathlike object or string representing an existing file
An optional white matter mask.
out_prefix : a unicode string
Output prefix for file names.

ad_file : a pathlike object or string representing an existing file color_fa_file : a pathlike object or string representing an existing file fa_file : a pathlike object or string representing an existing file md_file : a pathlike object or string representing an existing file out_file : a pathlike object or string representing an existing file rd_file : a pathlike object or string representing an existing file

TensorMode

Link to code

Bases: DipyDiffusionInterface

Creates a map of the mode of the diffusion tensors given a set of diffusion-weighted images, as well as their associated b-values and b-vectors [1]. Fits the diffusion tensors and calculates tensor mode with Dipy.

Example

>>> import nipype.interfaces.dipy as dipy
>>> mode = dipy.TensorMode()
>>> mode.inputs.in_file = 'diffusion.nii'
>>> mode.inputs.in_bvec = 'bvecs'
>>> mode.inputs.in_bval = 'bvals'
>>> mode.run()                                   # doctest: +SKIP

References

[1]Daniel B. Ennis and G. Kindlmann, “Orthogonal Tensor Invariants and the Analysis of Diffusion Tensor Magnetic Resonance Images”, Magnetic Resonance in Medicine, vol. 55, no. 1, pp. 136-146, 2006.
in_bval : a pathlike object or string representing an existing file
Input b-values table.
in_bvec : a pathlike object or string representing an existing file
Input b-vectors table.
in_file : a pathlike object or string representing an existing file
Input diffusion data.
b0_thres : an integer (int or long)
B0 threshold. (Nipype default value: 700)
mask_file : a pathlike object or string representing an existing file
An optional white matter mask.
out_prefix : a unicode string
Output prefix for file names.

out_file : a pathlike object or string representing an existing file