Does it run with the --cpu flag? That will run it with the cpu and thus isolate your problem to the gpu/cuda

On 9/9/2024 10:31 PM, Matthew Lynch wrote:

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I run this command:

mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test

and it fails with the following (partial) error message:

Node: 'model_3/unet_conv_downarm_0_0/Conv3D'
DNN library is not found.

which I assume means it cannot access the appropriate the CuDNN library.

I have installed

GPU: nvidia geforce RTX 3050 Ti (4Gb)
WSL2
Linux kernel: 5.15.153.1-microsoft-standard-WSL2 (after recent wsl --update)
CUDA Version 12.6
Windows Nvidia Driver version 560.94
CuDNN Version 9.4.0 installed in WSL, with libraries located in /lib/x86_64-linux-gnu

However, freesurfer's tensorflow seems to point to its own cudnn libraries in:
/usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/nvidia/cudnn/lib

including

libcudnn.so.8

which I assume is CuDNN version 8, and may not be compatible with CUDA 12.6?

Is there a way I can get freesurfer's script to use the CuDNN 9.4.0 that are installed globally on the WSL system?  Any other suggestions on what might be causing this error and how to fix it?


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