Hello everyone! My name is Oviya, I’m an undergrad hoping to get a bit of help.
I have been trying extract features from MRI images via a compute cluster, and have been successful with downsampled (250um) images (41MB). However, I am unable to run the same script on the native 100um resolution (542 MB). On the 100um resolution, I’ve been able to extract GLCM, GLSZM, NGTDM, and GLDM, but not GLRLM.
Tech support from the compute cluster indicated that the job is failing with a segmentation fault (exit code 139), which indicates a low-level crash in compiled code (e.g., ITK/SimpleITK/PyRadiomics or NumPy C extensions), not a Python exception.
From the logs, PyRadiomics completes feature extraction successfully (“Reading feature maps: 100%”), and the crash occurs immediately afterward during post-processing. So the failure might be happening in the step where extracted feature maps are converted into arrays and assembled into a feature matrix, or during cleanup between chunks.
I’m unsure of how to resolve this. If anyone could take a peek at the code/offer advice, it would be appreciated!
