miblab.totseg

miblab.totseg(vol, cutoff=None, **kwargs)

Run totalsegmentator on one or more volumes.

Source: totalsegmentator.

Parameters:

• vol (vreg.Volume3D or list) – Either a single volume, or a list of volumes to be segmented.

• cutoff (float, optional) – Pixels with a probability higher than cutoff will be included in the mask. If cutoff is not provided, probabilities will be returned directly. Defaults to None.

• kwargs – Any keyword arguments accepted by the totalsegmentor python API.

Returns:

A vreg volume with the label image. See totalsegmentator documentation for a dictionary mapping labels to anatomical structures.

Return type:

vreg.Volume3D

Example

Use a machine with a cpu to run the task ‘total_mr’ on a single volume saved as a nifti file:

>>> import miblab
>>> import vreg
>>> vol = vreg.read_nifti('path/to/volume.nii.gz')
>>> label = miblab.totseg(vol, cutoff=0.01, task='total_mr', device='cpu')
>>> vreg.write_nifti(label, 'path/to/label.nii.gz')