I was able to install on Windows 10 by more or less following the installation instructions at
https://docs.monai.io/projects/label/en/latest/installation.html
with the following modifications:
- I installed to a conda environment
- I installed the weekly monailabel instead of the stable version because installing the stable failed due (I think) to this issue: Unsuccessful `pip install monailabel>=0.4*` on Windows platform · Issue #719 · Project-MONAI/MONAILabel · GitHub, which is marked as resolved, but maybe hasn’t made it into the stable version yet
# From an "Anaconda Prompt" console window
# Create conda environment named "monaiweekly"
conda create --name monaiweekly python=3.9
conda activate monaiweekly
# Follow install process steps from monailabel website
python -m pip install --upgrade pip setuptools wheel
pip install torch==1.9.0+cu111 torchvision==0.10.0+cu111 torchaudio===0.9.0 -f https://download.pytorch.org/whl/torch_stable.html
python -c "import torch; print(torch.cuda.is_available())"
# ^^ above line should return true ^^
# Install monailabel
pip install monailabel-weekly
# "pip install monailabel" failed due to SimpleCRF error, fixed in weekly
# Download radiology app for monailabel
monailabel apps --download --name radiology --output apps
# Download sample data set (~27 GB, FYI)
monailabel datasets --download --name Task03_Liver --output datasets
# Start monailabel server
monailabel start_server --app apps/radiology --studies datasets/Task03_Liver/imagesTr --conf models deepedit
Initially, I had some problems due, I think, to having installed previous versions of torch, monailabel, or some combination of the two, but these were resolved when I uninstalled the old versions and then reinstalled the new versions in this new clean conda environment.
In Slicer, I got the MONAILabel extension and restarted Slicer, then was able to connect to the locally running server (by just pressing the fetch/refresh button on the MONAI Label server line of the MONAILabel module in Slicer) . I think an initial image volume from the liver data set was automatically loaded when I connected to the server, but if not, one was loaded when I hit the Next Sample button.
So far, so good. For the next steps, I got a little lost in how things were supposed to work. I have not been able to get a liver segmentation model working yet, but now that I think all the back end stuff is working, I am going to reread this thread and other similar ones to see if I can figure out how to do what I want. For reference, I have a dataset of 20 liver segmentations with corresponding images as a starting point as well as some more images without segmentations which I would like to begin to segment using MONAILabel, then refine those segmentations and contribute back to improve the training of the model. I think this is exactly what MONAILabel is supposed to be for, but there is very very limited documentation, so it is not at all clear how to actually do this. If I figure it out, I’ll post back here, and if I can’t figure it out I will share the sticking points.