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¶
Bases: NiftySegCommand
Wrapped executable:
seg_FillLesions
.Interface for executable seg_FillLesions from NiftySeg platform.
Fill all the masked lesions with WM intensity average.
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'
- Mandatory Inputs
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).- Optional Inputs
args (a 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) – 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) – 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
.- Outputs
out_file (a pathlike object or string representing a file) – Output segmentation.