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CCI-Bonn / HD-GLIO

Automated deep-learning based brain tumor segmentation on MRI
Apache License 2.0
26 stars 7 forks source link

Segmentation Labels #12

Closed smcch closed 1 year ago

smcch commented 1 year ago

Thank you to the author for providing this outstanding tool. I was able to successfully run the code on several preoperative MRI scans. However, when I checked the segmentation file, I noticed that I only obtained two labels: Contrast enhancing tumor and T2/FLAIR signal alteration. Can you explain why this might be happening?

Operating System: Ubuntu 20.04.4 LTS - WSL 2 Python Version: 3.7

Thanks!

FabianIsensee commented 1 year ago

Hi, this is because the model was only trained with those two labels. If you need a label for necrosis as well, I can recommend our docker for BraTS2020: https://hub.docker.com/r/fabianisensee/isen2020 Read also: https://github.com/BraTS/Instructions (unfortunately very outdated with docker links, but instructions are OK) Best, Fabian

smcch commented 1 year ago

I will definitely test out your Docker. Thank you for your quick response. Best regards