calc_vesselness_mask_from_quantiled_vesselness#

petpal.preproc.segmentation_tools.calc_vesselness_mask_from_quantiled_vesselness(input_image: ants.core.ANTsImage, min_quantile: float = 0.99, morph_dil_radius: int = 0, z_crop: int = 3) → ants.core.ANTsImage#

Generates a binary vesselness mask from a given vesselness image using quantile-based thresholding.

This function creates a binary mask by thresholding a vesselness image at a specified quantile of non-zero voxel values. Additionally, it allows for optional z-axis cropping and morphological dilation to refine the mask.

Parameters:

  • input_image (ants.core.ANTsImage) – Input vesselness image.

  • min_quantile (float, optional) – Minimum quantile value for voxel thresholding (default: 0.99). Must be in the range [0, 1).

  • morph_dil_radius (int, optional) – Radius for morphological dilation to refine the mask (default: 0). No dilation is applied if set to 0.

  • z_crop (int, optional) – Number of slices to crop from the z-axis from the bottom (default: 3).

Returns:

ants.core.ANTsImage – Binary vesselness mask.

Notes

  • The input image must be an ANTs image containing vesselness measures.

  • The quantile value (min_quartile) determines the threshold value based on non-zero voxel intensities.

  • If z_crop is greater than 0, the z-axis is cropped from the top and bottom.

  • Morphological dilation is applied to the binary mask with the specified radius, if provided.

Raises:

  • - AssertionError – If the input image is not 3D.

  • - AssertionError – If the provided quantile is not in the range [0, 1].

  • - AssertionError – If the provided z-crop is larger than the number of z-slices in the input image.