Segmentation Tools

Methods applying to segmentations.

Available methods: * combine_regions_as_mask(): Merge regions in a segmentation image into a mask with value 1 * resample_segmentation(): Resample a segmentation image to the affine of a 4D PET image. * vat_wm_ref_region(): Compute the white matter reference region for the VAT radiotracer.

Functions

combine_regions_as_mask(→ ants.core.ANTsImage)	Create a mask from a segmentation image and one or more labels.
segmentations_merge(→ numpy.ndarray)	Merge segmentations by assigning regions to a primary segmentation image from a secondary
binarize(input_image_numpy[, out_val])	Convert a segmentation image array into a mask by setting nonzero values
parcellate_right_left(→ numpy.ndarray)	Divide a region within a segmentation image into right and left values.
replace_probabilistic_region(segmentation_numpy, ...)	Runs a correction on a segmentation by replacing a list of regions with
resample_segmentation(input_image_path, ...)	Resamples a segmentation image to the resolution of a 4D PET series image. Takes the affine
vat_wm_ref_region(→ ants.ANTsImage)	Generates the cortical white matter reference region described in O'Donnell
eroded_wm_segmentation(→ ants.ANTsImage)	Generates eroded white matter region on a segmentation image and merges it into the image,
vat_wm_region_merge(wmparc_segmentation_path, ...[, ...])	Merge subcortical structures into a merged segmentation image according to
gw_segmentation(freesurfer_path, dseg_path, output_path)	Creates a gray matter and a white matter mask based on FreeSurfer regions. Useful for PVC.
subcortical_mask(input_seg_path[, output_seg_path, ...])	Gets a mask for subcortical regions from a FreeSurfer label image.
calc_vesselness_measure_image(→ ants.core.ANTsImage)	Computes a vesselness measure image using Hessian-based objectness filtering.
calc_vesselness_mask_from_quantiled_vesselness(...)	Generates a binary vesselness mask from a given vesselness image using quantile-based
unique_segmentation_labels(→ numpy.ndarray)	Get a list of unique ROI labels in a segmentation image.
seg_crop_to_pet_fov(.eps) → ants.ANTsImage)	Zero out segmentation values that lie outside of the PET FOV.