hey all, I’m having an error while trying to use the ‘total segmentator’ module. Traceback (most recent call last): File “C:\Users\dror\AppData\Local\NA-MIC\Slicer 5.2.1\bin\Python\slicer\util.py”, line 2961, in tryWithErrorDisplay yield File “C:/Users/dror/AppData/Local/NA-MIC/Slicer 5.2.1/NA-…

Please “Upgrade” the Totalsegmentator package first from the extension, now with running public WLAN. [image] If that does not help, you could pip install missing packages from the Python Interactor like this: slicer.util.pip_install("nibabel")

Some steps further:-) Still an error: Processing started Writing input file to C:/Users/Ronald/AppData/Local/Temp/Slicer/__SlicerTemp__2022-12-28_17+54+58.904/total-segmentator-input.nii Creating segmentations with TotalSegmentator AI… Total Segmentator arguments: [‘-i’, ‘C:/Users/Ronald/AppDat…

No personal experience, but yes, you may want to try that, uninstall PyTorch with the extension and reinstall it in CPU mode: [image] Please let us know how it works.

Dear Rudolf It works! Many thanks for your help and suggestions. It is relatively fast (even with CPU) and worked quite well even for a low dose CT (done along with a PET scan)…so it generates quite well segmentations for a poor quality scan. Regards Ronald

@rbumm Does total segmentator require cuDNN beyond regular cuda installation? I am getting this error message on Ubuntu 22.04 with Slicer 5.2.1. Cuda 12.0 is installed, and pytorch extension installed cu118 enabled torch. Traceback (most recent call last): File "/home/exouser/Slicer/bin/Python/s…

Hi I think you need CUDA 11.6 or 11.7 [image] PyTorch An open source machine learning framework that accelerates the path from research prototyping to production deployment. Hope it helps

Thanks I already got the cuda part taken care of. PyTorch worked fine. The issue was indeed the missing cuDNN library, which is not part of the CUDA package and you actually have to register with Nvidia, agree to their terms and download it. https://docs.nvidia.com/deeplearning/cudnn/install-guide/i…

@muratmaga great that it works now, on my windows systems cudnn and it´s folders seem to be present automatically on every Python where TotalSegmentator is installed, and there has never be the need for separate downloads. Would be interesting to find out why it was necessary on your system …

I use Windows, too, and I don’t remember ever having to manually install cuDNN either. Nobody else has reported this issue until now either. So, probably this manual cuDNN installation is only needed on certain Linux systems.

I’ve run into this before too. The Nvidia cuDNN instructions clearly say you need to get it via the developer program for both windows and linux: Installation Guide - NVIDIA Docs ). But apparently this is bundled in pytorch: How to check if torch uses cuDNN - #3 by timonbimon - PyTorch Forums “if…

Error While using 'Total Segmentator'

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Error While using 'Total Segmentator'

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