interfaces.niftyseg.patchmatch

PatchMatch

Link to code

Wraps 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.

Source code | Documentation

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]
database_file: (an existing file name)
        Database with the segmentations
        flag: -db %s, position: 3
in_file: (an existing file name)
        Input image to segment
        flag: -i %s, position: 1
mask_file: (an existing file name)
        Input mask for the area where applies PatchMatch
        flag: -m %s, position: 2

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
cs_size: (an integer (int or long))
        Constrained search area size, number of times bigger than the
        patchsize
        flag: -cs %i
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
it_num: (an integer (int or long))
        Number of iterations for the patchmatch algorithm
        flag: -it %i
match_num: (an integer (int or long))
        Number of better matching
        flag: -match %i
out_file: (a file name)
        The output filename of the patchmatch results
        flag: -o %s, position: 4
patch_size: (an integer (int or long))
        Patch size, #voxels
        flag: -size %i
pm_num: (an integer (int or long))
        Number of patchmatch executions
        flag: -pm %i

Outputs:

out_file: (a file name)
        Output segmentation