nipype.interfaces.dipy.preprocess module¶
Denoise¶
Bases: DipyBaseInterface
An interface to denoising diffusion datasets [Coupe2008]. See http://nipy.org/dipy/examples_built/denoise_nlmeans.html#example-denoise-nlmeans.
[Coupe2008]Coupe P et al., An Optimized Blockwise Non Local Means Denoising Filter for 3D Magnetic Resonance Images, IEEE Transactions on Medical Imaging, 27(4):425-441, 2008.
Example
>>> import nipype.interfaces.dipy as dipy >>> denoise = dipy.Denoise() >>> denoise.inputs.in_file = 'diffusion.nii' >>> denoise.run()
- in_filea pathlike object or string representing an existing file
The input 4D diffusion-weighted image file.
- noise_model‘rician’ or ‘gaussian’
Noise distribution model. (Nipype default value:
rician
)
- block_radiusan integer
Block_radius. (Nipype default value:
5
)- in_maska pathlike object or string representing an existing file
Brain mask.
- noise_maska pathlike object or string representing an existing file
Mask in which the standard deviation of noise will be computed.
- patch_radiusan integer
Patch radius. (Nipype default value:
1
)- signal_maska pathlike object or string representing an existing file
Mask in which the mean signal will be computed.
- snra float
Manually set an SNR.
out_file : a pathlike object or string representing an existing file
Resample¶
Bases: DipyBaseInterface
An interface to reslicing diffusion datasets. See http://nipy.org/dipy/examples_built/reslice_datasets.html#example-reslice-datasets.
Example
>>> import nipype.interfaces.dipy as dipy >>> reslice = dipy.Resample() >>> reslice.inputs.in_file = 'diffusion.nii' >>> reslice.run()
- in_filea pathlike object or string representing an existing file
The input 4D diffusion-weighted image file.
- interpan integer
Order of the interpolator (0 = nearest, 1 = linear, etc. (Nipype default value:
1
)
- vox_sizea tuple of the form: (a float, a float, a float)
Specify the new voxel zooms. If no vox_size is set, then isotropic regridding will be performed, with spacing equal to the smallest current zoom.
out_file : a pathlike object or string representing an existing file
- nipype.interfaces.dipy.preprocess.nlmeans_proxy(in_file, settings, snr=None, smask=None, nmask=None, out_file=None)¶
Uses non-local means to denoise 4D datasets
- nipype.interfaces.dipy.preprocess.resample_proxy(in_file, order=3, new_zooms=None, out_file=None)¶
Performs regridding of an image to set isotropic voxel sizes using dipy.