Project-MONAI/tutorials

Auto3dseg multi labels

Malitha123 opened this issue · 7 comments

Malitha123 commented

I have a segmentation task with 3 labels. May I know how to segment it using Auto3Dseg? All the examples are for one label tasks.

diazandr3s commented

Hi @Malitha123,

I'd recommend you follow this example for multi-label segmentation tasks: https://github.com/Project-MONAI/tutorials/tree/main/auto3dseg/tasks/btcv

Which organs/tissues do you want to segment?

Malitha123 commented

I am working on my own dataset for heart segmentation with consists of 5 labels (LA, RA, and so on). Those masks are in separate folders. For example Patient001 has 5 masks.

  • 👍1
diazandr3s commented

Hi @Malitha123,

The first step should be merging the masks into a single file. Then create the YAML and JSON files to train Auto3DSeg.
Make sure the label indexes are in consecutive order and consistent throughout the dataset. i.e. LA is always 1, RA is 2, ...

Hope this helps,

NastaranVB commented

Hi @diazandr3s ,
In my segmentation task, there are 2 labels: infarction and hemorrhage parts in brain CT images. (3 labels when considering the brain as background). I would be thankful if you could also tell me which segmentation example fits my task more accurately.

diazandr3s commented

Hi @NastaranVB,

Are the segments overlapping? Have you seen this tutorial? https://github.com/Project-MONAI/tutorials/tree/main/auto3dseg/tasks/kits23

NastaranVB commented

Hi @diazandr3s,
Thanks for getting back in touch.
yes, they are overlapping.

diazandr3s commented

Hi @NastaranVB,

Thanks!
I think this is the best example for this sort of task: https://github.com/Project-MONAI/tutorials/blob/main/auto3dseg/tasks/kits23/input.yaml

Hope this helps,