Skull-Data-Processing

Python/Matlab scripts to segment human skull bone from CT scan , clean the segmented skull, convert the skull volume to mesh and inject holes to the healthy skull.

• Python 3.6
• MATLAB R2018b
• MeshLab v2016.12
• ITK-SNAP 3.6.0
• 3D Slicer 4.8.1 r26813

segment skull from CT scan

• dependency : pynrrd, pydicom.
• installation : pip install pynrrd , pip install -U pydicom
• usage :
  1. change directory
  2. run in the command window: python segmentation.py
• note : the script can read dicom files exported directly from CT machine for segmentation and can also read nrrd files converted from dicom files using 3D Slicer.

skull data cleaning

• dependency : 3D connected component analysis.
• installation : pip install connected-components-3d
• usage :
  1. change data_dir and save_dir to where you stored the original nrrd files and where you want to save the cleaned nrrd files to.
  2. run in the command window: python denoising.py

artificial defect injection

• dependency : PyMRT.
• installation : pip install pymrt
• usage :
  1. change pair_list : where you storied the cleaned nrrd files (it's recommended that skull data cleaning performed before defect injection). defected_dir : where to store the skull with defect to. implant_dir : where to store the removed part (i.e., the implant) to.
  2. specify the size of defect to be injected into the skull, 128 recommended.
  3. run in the command window: python defectinject.py
• note: the current code provide functionalities to generate cubic defect generate_cude(defect_size) and spherical dfects generate_sphere(defect_size).

create skull mesh model from .nrrd files

• dependency : Open3D, scikit-image, PyMCubes.
• installation : pip install open3d pip install scikit-image pip install --upgrade PyMCubes
• usage :
  python nrrd2mesh.py

voxelization : create voxel grid from mesh (matlab/python)

• dependency : Polygon2Voxel, stlread.
• usage :
  [F,V] = stlread('skullmesh.stl');
FV.faces=F;
FV.vertices=V;
Volume=polygon2voxel(FV,512,'none',true);
  save Volume.mat to nrrd
  import scipy.io as sio, import nrrd
volume=sio.loadmat('Volumen.mat')['Volume']
nrrd.write('volume.nrrd',volume.astype(float64))