vcasellesb / stl2nii

.stl to .nii(.gz) file converter

STL to NIFTI file converter

This Python file will convert your STL meshes into NIFTI files. This "tool" is intended for researchers working on biomedical imaging, so the code is structured in a way that requires you to provide an input image to map the "labels" to. Please, if you've found this code useful don't forget to give it a star!

WARNING: Default setting casts the output NIFTI numpy array to uint8. To change this behavior, use the -dtype flag.

Usage

python3 /path/to/stl2nii \
    -i [.stl file(s)] \
    -ref [.nii/.nii.gz file to map stl to its space (usually the image the stl comes from)] \
    -o [/path/to/desired/output/folder]

Example Usage:

Let's say I want to convert a bunch of STL meshes I've obtained by segmenting the image corresponding to patient 225 using my favourite automatic segmentation tool. These are in my Downloads folder, and I want to generate NIFTI files mapped to the original image. I'd do it like this:

python3 ~/work/research/stl2nii \
    -i ~/Downloads/P225/*.stl \
    -ref data/P225/image/data_P225.nii.gz \
    -o data/P225/labels/nii

stl2nii's Issues

Code Efficiency Recommendations

Thanks for your great jobs!
I found this code to be very inefficient:

for i in range(image.GetNumberOfPoints()):
image.GetPointData().GetScalars().SetTuple1(i, inval)

Maybe you can try the following code:

scalars = image.GetPointData().GetScalars()

from vtkmodules.util.numpy_support import vtk_to_numpy

scalar_array = vtk_to_numpy(scalars)

scalar_array[:] = inval

scalars.Modified()

The result is not quite right

thanks your works, i have one stl file label, want to convert .nii file. i only Modify the following code。but result is not quite。