BraTS-Toolkit
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Preprocessor stuck on running HD-Bet
Hi, I'm trying to use the BraTS preprocessor, and it is getting stuck on the "running HD-Bet." Does anyone face this issue before when using this preprocessor? Thank you! I will provide the required information to help you figure it out!
Attachment from the output command line
Thank you!
thanks for your interest in btk. Can you provide information about your hardware? Also run the nvidia docker toolkit hello-world please and post the output here.
Sure! Thanks for the quick reply!
Here is the docker hello-world response:
nvidia-smi response:
running a base CUDA container:
Hardware information: I used cloud computing instance under our university cloud environment:
- OS: Linux ubuntu focal 20.04
- RAM: 16GB
- vCPUs: 8
- GPU: NVIDIA A100-SXM
Sorry, I believe there might be a misunderstanding, please run:
docker run --rm --gpus all nvidia/cuda:11.0-base nvidia-smi
You might need sudo depending on your docker configuration.
from: https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html
closing until more details are provided, feel free to reopen.
Hi, I have the same problem. I am running ubuntu 22.04.1 with CUDA 12.0 on WSL2 in Windows 11 and the Toolkit is also stuck on "running HD-Bet".
@chocolatetoast-chiu Did you manage to find a solution in the meantime?
The output of the nvidia-smi command looks fine so I am not sure what went wrong.
Please let me know if I should provide more details. Thank you !
Sorry, I overlooked your msg @azounek . Did you find a solution int he meantime? Potentially the same issue as here: https://github.com/neuronflow/BraTS-Toolkit/issues/29
Perhaps a good test would be whether HD-BET alone can run on your machines: https://github.com/MIC-DKFZ/HD-BET
@FabianIsensee do you have an idea what could be the issue here?
Sorry for not following this issue for a long time!
I did solve this issue by setting the mode to GPU.
# execute it
prep.single_preprocess(
t1File=t1File,
t1cFile=t1cFile,
t2File=t2File,
flaFile=flaFile,
outputFolder=outputDir + examName,
# this way the brain extraction will run on cpu
mode="gpu",
confirm=False,
skipUpdate=False,
gpuid="0",
)
If the mode was set to 'cpu', then I'm not able to finish my preprocessing. I don't know the exact reason why.
Interesting. We have a new preprocessing pipeline now that might solve your problems. Let me know if you want to serve as a beta tester.
closed until further details about the cpu
mode are provided.