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_file : a pathlike object or string representing an existing file

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

lesion_mask : a pathlike object or string representing an existing file

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

args : a unicode string

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

bin_mask : a pathlike object or string representing a file

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

cwf : a float

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

debug : a boolean

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

environ : a 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_dilation : an integer (int or long)

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

match : a float

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

other : a 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_datatype : a string

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

out_file : a 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).

search : a float

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

size : an integer (int or long)

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

smooth : a float

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

use_2d : a boolean

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

verbose : a boolean

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

out_file : a pathlike object or string representing a file

Output segmentation.