Hello!! Thank you so much for your reply!
The file I am working with is a micro-CT of a plant seed sample, and I am trying to separate the morphology inside to get the volumetric data of each part.
So the pathology app did not fit my purpose.
I needed to change the labels and disable the use_pretrained_model so it would not use the given labels.
When I changed the labels and disable the use_pretrained_model so it would not use the given labels in “MONAILabel/monailabel/deepedit/multilabel/transforms.py” and “MONAILabel/sample-apps/radiology/lib/configs/deepedit.py”, the changes weren’t reflected on the 3D Slicer and gave me the original label such as spleen, liver and etc.
That is why I had to copy the radiology folder and make a new one.
I think the term histology may have caused the confusion.
Sorry about that.
I started the server(big thanks to you) and successfully changed the labels using the given information from the forum.
$Env:PATH += “;C:\Users\njy95\MONAILabel\monailabel\scripts”
monailabel start_server --app C:/Users/njy95/MONAILabel/sample-apps/histology --studies C:/Users/njy95/datasets/Task11_BR/imagesTr --conf models deepedit --port 8000 --host 127.0.0.1
However, I don’t know my dataset’s target spacing and spatial size for the pretraining process.
To be honest, I don’t clearly understand what target_spacing and spatial_size are. I am assuming this is different from the actual pixel value and was hoping that the heuristic planner would give be recommended value.
That is why I used --conf heuristic_planner true, but it did not work.
Can you give me a advise on what the problem could be?