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mlcommons / GaNDLF

A generalizable application framework for segmentation, regression, and classification using PyTorch
https://gandlf.org
Apache License 2.0
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[BUG] SimpleITK version 2.3.0 causes errors #894

Closed Linardos closed 1 month ago

Linardos commented 3 months ago

Describe the bug

There is an issue with running the Fets Challenge pertaining to SimpleITK. image

To Reproduce

Steps to reproduce the behavior:

  1. Data used is that of FeTS challenges 2022 and 2024 (https://www.synapse.org/Synapse:syn29264504)
  2. To reproduce the behavior, follow the instructions: https://github.com/FeTS-AI/Challenge/tree/main/Task_1

Environment information

This happened both in WSL and in a VirtualBox Linux environment GaNDLF version according to pip freeze gives me this: GANDLF @ git+https://github.com/CBICA/GaNDLF.git@e4d0d4bfdf4076130817001a98dfb90189956278

Solution:

The issue was caused by SimpleITK 2.3.0. I tried and it works if I install simpleITK version 2.2.0 or 2.2.1

sarthakpati commented 3 months ago

Hmm, the latest CI runs (<3 months) seem to be using 2.3.1, and all are running without issue. I was unable to replicate this issue on 2 of my WSL systems or on my local machine. Is it possible that this was because some underlying system library was missing? I am unsure how to proceed. Any ideas?

sarthakpati commented 1 month ago

Can you check if you are seeing the same issues with SimpleITK 2.4.0 as well?

sarthakpati commented 1 month ago

This seems to be related to the underlying system GLIB version. The best way to handle this would be to update it, unless the SimpleITK folks can say something otherwise on their forum. Another potential solution is explained on this thread: https://github.com/ContinuumIO/anaconda-issues/issues/7640

I am closing this thread out, please re-open or create a new issue if you run into anything else.