ants.ops.get_mask

get_mask(image, low_thresh=None, high_thresh=None, cleanup=2)[source]

Get a binary mask image from the given image after thresholding

ANTsR function: getMask

Parameters:

  • image (ants.core.ANTsImage) – image from which mask will be computed. Can be an antsImage of 2, 3 or 4 dimensions.

  • low_thresh (scalar (optional)) – An inclusive lower threshold for voxels to be included in the mask. If not given, defaults to image mean.

  • high_thresh (scalar (optional)) – An inclusive upper threshold for voxels to be included in the mask. If not given, defaults to image max

  • cleanup (int) –

    If > 0, morphological operations will be applied to clean up the mask by eroding away small or weakly-connected areas, and closing holes. If cleanup is >0, the following steps are applied

    1. Erosion with radius 2 voxels

    2. Retain largest component

    3. Dilation with radius 1 voxel

    4. Morphological closing

Return type:

ants.core.ANTsImage

Example

>>> import ants
>>> image = ants.image_read( ants.get_ants_data('r16') )
>>> mask = ants.get_mask(image)