# Creating a closed 3D .stl from Nifti segmentations

**URL:** https://discourse.vtk.org/t/creating-a-closed-3d-stl-from-nifti-segmentations/15203
**Category:** Support
**Tags:** python
**Created:** [January 23, 2025, 7:04pm UTC](https://discourse.vtk.org/t/creating-a-closed-3d-stl-from-nifti-segmentations/15203 "2025-01-23T19:04:20Z")
**Posts on this page:** 1
**Page:** 1

<div class="post-metadata">

### Author: ![Nikolair1](https://discourse.vtk.org/user_avatar/discourse.vtk.org/nikolair1/32/9746_2.png) [@Nikolair1](https://discourse.vtk.org/u/Nikolair1)
#### Post date: [January 23, 2025, 7:04pm UTC](https://discourse.vtk.org/t/creating-a-closed-3d-stl-from-nifti-segmentations/15203/1 "2025-01-23T19:04:20Z")

</div>

Hi, I’m working on creating a segmentation pipeline and am having issues with creating a closed .stl file from my segmentations. The code block is below and here is a picture of the .stl that is created. As you can see it looks good from the top view.

 ![image](https://discourse.vtk.org/uploads/default/original/2X/8/84325051f4938abc5414f3d295f1500b3a590bfc.png)  
However, the bottom view isn’t closed and the outer rings aren’t interpolating to the inner one.  
 ![image](https://discourse.vtk.org/uploads/default/original/2X/b/b9034a53f48eb6121a9ff471ac5593d0f1ddcdc1.png)  
The desired bottom should be something like this (taken in 3D Slicer)  
 ![image](https://discourse.vtk.org/uploads/default/original/2X/c/ce4254efa822271173e605257ddec7f245e36723.png)  
Any help is appreciated!  
Code:

```auto
def process_nifti_files_to_stl(self):
        nifti_path = os.path.join('combined_output', 'combined_volume.nii.gz')
        if not os.path.exists(nifti_path):
            QMessageBox.warning(self, "File Not Found", "No combined NIfTI file found. Please create it first.")
            return
        sitk_image = sitk.ReadImage(nifti_path)
        image_array = sitk.GetArrayFromImage(sitk_image)
        input_image = image_from_array(image_array)
        interpolated_image = morphological_contour_interpolation(
            input_image=input_image,
            label=1,
            axis=-1,
            no_heuristic_alignment=False,
            no_use_distance_transform = False,
            use_custom_slice_positions=False,
            no_use_extrapolation=False,
            use_ball_structuring_element=False
        )
        interpolated_array = interpolated_image.data
        vtk_image = vtk.vtkImageData()
        depth, height, width = interpolated_array.shape
        vtk_image.SetDimensions(width, height, depth)
        vtk_image.SetSpacing(sitk_image.GetSpacing())
        flat_image_array = interpolated_array.flatten()
        vtk_data_array = numpy_to_vtk(num_array=flat_image_array, deep=True, array_type=vtk.VTK_FLOAT)
        vtk_image.GetPointData().SetScalars(vtk_data_array)

        print(vtk_image.GetNumberOfPoints())
        print(vtk_image.GetPointData().GetScalars().GetRange())

        gaussianRadius = 0.75
        gaussianStandardDeviation = 1.5
        gaussian = vtk.vtkImageGaussianSmooth()
        gaussian.SetInputData(vtk_image)
        gaussian.SetStandardDeviations(
            gaussianStandardDeviation,
            gaussianStandardDeviation,
            gaussianStandardDeviation
        )
        gaussian.SetRadiusFactors(gaussianRadius, gaussianRadius, gaussianRadius)
        gaussian.Update()

        print(gaussian.GetOutput().GetNumberOfPoints())
        print(gaussian.GetOutput().GetPointData().GetScalars().GetRange())

        isoValue = gaussian.GetOutput().GetPointData().GetScalars().GetRange()[1] / 2 # Adjust as needed
        use_flying_edges = True
        if use_flying_edges:
            print("Using vtkFlyingEdges3D for isosurface extraction.")
            iso_surface = vtk.vtkFlyingEdges3D()
        else:
            print("Using vtkMarchingCubes for isosurface extraction.")
            iso_surface = vtk.vtkMarchingCubes()
        iso_surface.SetInputConnection(gaussian.GetOutputPort())
        iso_surface.ComputeScalarsOff()
        iso_surface.ComputeGradientsOff()
        iso_surface.ComputeNormalsOff()
        iso_surface.SetValue(0, isoValue)
        iso_surface.Update()

        smoothingIterations = 20
        passBand = 0.001
        featureAngle = 60.0
        smoother = vtk.vtkWindowedSincPolyDataFilter()
        smoother.SetInputConnection(iso_surface.GetOutputPort())
        smoother.SetNumberOfIterations(smoothingIterations)
        smoother.BoundarySmoothingOff()
        smoother.FeatureEdgeSmoothingOff()
        smoother.SetFeatureAngle(featureAngle)
        smoother.SetPassBand(passBand)
        smoother.NonManifoldSmoothingOn()
        smoother.NormalizeCoordinatesOn()
        smoother.Update()
        final_poly_data = smoother.GetOutput()

        stl_writer = vtk.vtkSTLWriter()
        stl_output_path = os.path.join('combined_output', 'combined_volume_smoothed.stl')
        stl_writer.SetFileName(stl_output_path)
        stl_writer.SetInputData(final_poly_data)
        stl_writer.Write()

```