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# nipype.interfaces.niftyseg.lesions module

Nipype interface for seg_FillLesions.

The fusion module provides higher-level interfaces to some of the operations that can be performed with the seg_FillLesions command-line program.

Examples

See the docstrings of the individual classes for examples.

## FillLesions

Link to code

> Bases: NiftySegCommand

> Wrapped executable: `seg_FillLesions`.

> Interface for executable seg_FillLesions from NiftySeg platform.

> Fill all the masked lesions with WM intensity average.

> Source code | Documentation

> Examples

>     >>> from nipype.interfaces import niftyseg
>     >>> node = niftyseg.FillLesions()
>     >>> node.inputs.in_file = 'im1.nii'
>     >>> node.inputs.lesion_mask = 'im2.nii'
>     >>> node.cmdline
>     'seg_FillLesions -i im1.nii -l im2.nii -o im1_lesions_filled.nii.gz'

> in_filea pathlike object or string representing an existing file

>   Input image to fill lesions. Maps to a command-line argument: `-i %s` (position: 1).

> lesion_maska pathlike object or string representing an existing file

>   Lesion mask. Maps to a command-line argument: `-l %s` (position: 2).

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> bin_maska pathlike object or string representing a file

>   Give a binary mask with the valid search areas. Maps to a command-line argument: `-mask %s`.

> cwfa float

>   Patch cardinality weighting factor (by default 2). Maps to a command-line argument: `-cwf %f`.

> debuga boolean

>   Save all intermidium files (by default OFF). Maps to a command-line argument: `-debug`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> in_dilationan integer

>   Dilate the mask <int> times (in voxels, by default 0). Maps to a command-line argument: `-dil %d`.

> matcha float

>   Percentage of minimum number of voxels between patches <float> (by default 0.5). Maps to a command-line argument: `-match %f`.

> othera boolean

>   Guizard et al. (FIN 2015) method, it doesn’t include the multiresolution/hierarchical inpainting part, this part needs to be done with some external software such as reg_tools and reg_resample from NiftyReg. By default it uses the method presented in Prados et al. (Neuroimage 2016). Maps to a command-line argument: `-other`.

> out_datatypea string

>   Set output <datatype> (char, short, int, uchar, ushort, uint, float, double). Maps to a command-line argument: `-odt %s`.

> out_filea pathlike object or string representing a file

>   The output filename of the fill lesions results. Maps to a command-line argument: `-o %s` (position: 3).

> searcha float

>   Minimum percentage of valid voxels in target patch <float> (by default 0). Maps to a command-line argument: `-search %f`.

> sizean integer

>   Search regions size respect biggest patch size (by default 4). Maps to a command-line argument: `-size %d`.

> smootha float

>   Smoothing by <float> (in minimal 6-neighbourhood voxels (by default 0.1)). Maps to a command-line argument: `-smo %f`.

> use_2da boolean

>   Uses 2D patches in the Z axis, by default 3D. Maps to a command-line argument: `-2D`.

> verbosea boolean

>   Verbose (by default OFF). Maps to a command-line argument: `-v`.

> out_filea pathlike object or string representing a file

>   Output segmentation.