interfaces.niftyseg.patchmatch¶
PatchMatch¶
Wraps the executable command seg_PatchMatch
.
Interface for executable seg_PatchMatch from NiftySeg platform.
The database file is a text file and in each line we have a template file, a mask with the search region to consider and a file with the label to propagate.
Input image, input mask, template images from database and masks from database must have the same 4D resolution (same number of XxYxZ voxels, modalities and/or time-points). Label files from database must have the same 3D resolution (XxYxZ voxels) than input image but can have different number of volumes than the input image allowing to propagate multiple labels in the same execution.
Examples¶
>>> from nipype.interfaces import niftyseg
>>> node = niftyseg.PatchMatch()
>>> node.inputs.in_file = 'im1.nii'
>>> node.inputs.mask_file = 'im2.nii'
>>> node.inputs.database_file = 'db.xml'
>>> node.cmdline
'seg_PatchMatch -i im1.nii -m im2.nii -db db.xml -o im1_pm.nii.gz'
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
Input image to segment
argument: ``-i %s``, position: 1
mask_file: (a pathlike object or string representing an existing
file)
Input mask for the area where applies PatchMatch
argument: ``-m %s``, position: 2
database_file: (a pathlike object or string representing an existing
file)
Database with the segmentations
argument: ``-db %s``, position: 3
[Optional]
out_file: (a pathlike object or string representing a file)
The output filename of the patchmatch results
argument: ``-o %s``, position: 4
patch_size: (an integer (int or long))
Patch size, #voxels
argument: ``-size %i``
cs_size: (an integer (int or long))
Constrained search area size, number of times bigger than the
patchsize
argument: ``-cs %i``
match_num: (an integer (int or long))
Number of better matching
argument: ``-match %i``
pm_num: (an integer (int or long))
Number of patchmatch executions
argument: ``-pm %i``
it_num: (an integer (int or long))
Number of iterations for the patchmatch algorithm
argument: ``-it %i``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing a file)
Output segmentation