xrayto3D-morphometry

This is a python package for extracting landmarks from pelvic segmentation volume and morphological parameters from Proximal femur.

For Pelvic Bone Segmentation This is a adaptation of [Fischer 2019] Fischer, M. C. M., Krooß, F., Habor, J. & Radermacher, K. - A robust method for automatic identification of landmarks on surface models of the pelvis. Scientific Reports, https://doi.org/10.1038/s41598-019-49573-4 (2019) from matlab to python.

Original MATLAB code: https://github.com/RWTHmediTEC/PelvicLandmarkIdentification

For Proximal Femur This is a adapted implementation from Cerveri, Pietro, et al. "Automated method for computing the morphological and clinical parameters of the proximal femur using heuristic modeling techniques." Annals of Biomedical Engineering 38 (2010): 1752-1766

For Vertebra Adapted from Di Angelo, Luca, and Paolo Di Stefano. "A new method for the automatic identification of the dimensional features of vertebrae." Computer methods and programs in biomedicine 121.1 (2015): 36-48.

Usage

python pelvic_landmarks_v2.py --file test_data/s0014_hip_msk_pred.nii.gz

{'ASIS_L': array([-79.967545, -21.783907, -50.073395], dtype=float32), 'ASIS_R': array([ 85.032455, -11.783906, -53.073395], dtype=float32), 'PT_L': array([-16.967546,  39.216095, -50.073395], dtype=float32), 'PT_R': array([ 13.032453,  44.216095, -50.073395], dtype=float32)}

python vertebra_landmarks.py test_data/sub-verse004_vert-23-seg-vert_msk.nii.gz

{'spl': 36.453527302556076, 'spa': 138.60229619651807, 'avbh': 26.23448596400926, 'pvbh': 23.378738362530747, 'svbl': 29.54202176642218, 'ivbl': 30.34065592251007, 'vcl': 13.27892594709724}