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Sllambias / yucca

Apache License 2.0
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Any Inference Example? #178

Closed Drwaish closed 2 months ago

Drwaish commented 2 months ago

Can anyone share any sample file for inference and pre-train model?

Thanks

Sllambias commented 2 months ago

Hi Drwaish,

Thanks for your interest!

I'm afraid I can't share any real images but many are available by applying to e.g. https://sites.wustl.edu/oasisbrains/. I can however supply a sample model trained on a subset of OASIS images through zenodo.

When you've downloaded the modelzip, it needs to be unzipped in the yucca_models folder that you've also specified in the environment variables. After unzipping it should look like "YOUR/PATH/TO/YUCCA_DATA/yucca_models/Task001_OASIS/...."

Afterwards, assuming you've set up an environment for Yucca according to the instructions on the frontpage readme, you can run inference by using the following command:

yucca_inference -s Task001 -d 2D -t OUTPUT_NAME --pred YOUR/PATH/TO/IMAGEDIR

Best, Sebastian

Drwaish commented 2 months ago

Thanks, Sebastian for your response.

Drwaish commented 2 months ago

Answered by Author so issue closed. Thanks