Mesh generation from NIFTI files using Python and C Libraries

Authors: Sacha Cruz, Mario Espinoza

Date: 28/01/2024

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|   NIFTI -> MESH GENERATION   |
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About the project

This script takes a single-labeled NIFTI file (.nii / .nii.gz) and converts it into a 3D mesh (.obj / .stl / .ply / .3ds).

More precisely, the code allows to :

• Create a 3D mesh from a NIFTI file
  • Choose the library (Pymeshlab, VTK or Nii2Mesh)
  • Set a mesh-smoothing value
  • Set a mesh-simplification value
• Show the mesh in a 3D object visualizer
• Store Mesh's details (Mesh volume, File size, etc.) in a TXT file

It uses already-existing libraries :

• Pymeshlab : (GitHub)
• VTK (Python) : (GitHub)
• Nii2mesh (C) : (GitHub)

Project hierarchy and files

1. The main code is under the folder : nii_mesh_generation README FILE HERE

   • The main function is on the nii_mesh_gen.py file
   • You can learn how it works on the test_nii_mesh_gen.py file
   • It calls functions from internal libraries :
     • mesh_gen_c.py : calls nii2mesh library made on C
     • mesh_gen_python.py : calls pymeshlab and vtk libraries
     • mesh_tools.py : provides useful tools for mesh visualization and details

2. The additional code is under the folder : additional_mesh_utils README FILE HERE

   • test_libraries_311.py --> Create a bunch of 3D objects (trying different libraries, methods and parameters)
   • objtools.py --> provides a lot of useful tools :
     • Visualize a 3D Mesh in a 3D interactiuve window
     • Save the current 3D view of a Mesh in a flat 2D image
     • Save the current Mesh's details in an excel file
     • Automatizate these functions to a whole folder containing different meshes
   • --> The purpose is to call the function showFolder in the folder where all the 3D meshes where created, to see every mesh one by one
   • test_mesh_simple.py --> tests the showObj function
   • test_mesh_folder.py --> tests the showFolder function

nii_mesh_generation

nii_mesh_gen.py
test_niimeshgen.py
source

mesh_gen_c
mesh_gen_python
mesh_tools

additional_mesh_utils

objtools.py
test_libraries_311.py
test_libraries_308.py