Registering a pair of binary masks Question: I’m trying to register a pair of binary masks, not a pair of images. To explain further, I’m trying to build a model that automatically strips the brain from the head skull. For the better model accuracy, I already have labeled the brain area using ITK-SNAP. I just …
Skull stripping with python/simpleITK Question: I’m trying to perform a skull stripping with simpleITK in python. I’m using the StripTsImageFilter function as follows: #upload data # Path of nii img path = r’C:UsersKateJupyterDataThesisPROGRESSION003fet.nii.gz’ # Read the .nii image with SimpleITK: img = sitk.ReadImage(path) #read atlas and atlasmap #Obtained from 3DSlicer documentation: https://www.slicer.org/wiki/Documentation/Nightly/Modules/SwissSkullStripper atlas = sitk.ReadImage(r’C:UsersKateJupyterthesisatlasImage.mha’) …
Difference between SimpleITK.Euler3DTransform and scipy.spatial.transform.Rotation.from_euler? Question: Using these two library functions: SimpleITK.Euler3DTransform scipy.spatial.transform.Rotation.from_euler to create a simple rotation matrix from Euler Angles: import numpy as np import SimpleITK as sitk from scipy.spatial.transform import Rotation from math import pi euler_angles = [pi / 10, pi / 18, pi / 36] sitk_matrix = sitk.Euler3DTransform((0, 0, 0), *euler_angles).GetMatrix() …
