Crash while generating meshes (access violation)

[MattTheCuber]

Hello, I have been generating meshes based on the segmentations from MSD. Once my script hit the Task05_Prostate labels, it started crashing seemingly randomly. It fails anywhere from the first to the 16th from my testing. I'm sure there is a pattern, but I couldn't find it. It succeeded on all my other datasets yesterday (Task01_BrainTumour, Task02_Heart, Task03_Liver, Task04_Hippocampus) without any problems, and there is no real difference from the working data to this data as far as size, data type, or scalar range.

When I enable fault handler, I get the following output:

Windows fatal exception: access violation

Current thread 0x00007704 (most recent call first):
  File "....\venv\Lib\site-packages\itk\ITKCommonBasePython.py", line 3115 in UpdateLargestPossibleRegion
  File "...\.venv\Lib\site-packages\itk\ITKCommonBasePython.py", line 3327 in __internal_call__
  File "...\.venv\Lib\site-packages\itk\itkCuberilleImageToMeshFilterPython.py", line 6444 in cuberille_image_to_mesh_filter
  File "...\.venv\Lib\site-packages\itk\support\helpers.py", line 157 in image_filter_wrapper
  ...

A simple producible script is shown below.

Download and extract the dataset: https://msd-for-monai.s3-us-west-2.amazonaws.com/Task05_Prostate.tar

import faulthandler
from pathlib import Path

import itk
import nibabel as nib

itk.Image  # implicitly load ITKCommon module

from itk.CuberillePython import cuberille_image_to_mesh_filter

faulthandler.enable()

for path in Path("Task05_Prostate/labelsTr").glob("*.nii.gz"):
    if path.name.startswith("._"):
        continue  # Skip macOS metadata files
    print(f"Processing {path}...")
    img = nib.load(path)
    data = img.get_fdata()
    cuberille_image_to_mesh_filter(data, project_vertices_to_iso_surface=False)

Environment

• Operating System: Windows 11
• Python Version: 3.13
• ITK Version: 5.4.4.post1
• ITKCuberille Version: 2.7.2

[MattTheCuber]

Ok, I just learned that if you change the argument to project_vertices_to_iso_surface=True, it always crashes on the first dataset:

prostate_00.nii.gz

New minimal reproducible example:

import faulthandler

import itk
import nibabel as nib

itk.Image  # implicitly load ITKCommon module

from itk.CuberillePython import cuberille_image_to_mesh_filter

faulthandler.enable()

img = nib.load("prostate_00.nii.gz")
data = img.get_fdata()
cuberille_image_to_mesh_filter(data)

[dzenanz]

I can reproduce this crash locally. I added this test case as the last commit in PR #80. There are no known resources to address these failures now. A possible workaround is to change the iso-value used.