Many thanks for the ping, @rbumm.
Just came back from leave, and I’m catching up on emails/discussions.
@JacobD all these are great questions. I see most of them have been addressed by @rbumm.
Here are my comments on them:
- Based on my goal of using previously segmented images to train a model, is the ‘segmentation’ model the best model to utilize? If not, why would the DeepGrow or DeepEdit be chosen alternatively?
Yes, I’d recommend starting with the Segmentation model.
DeepGrow and DeepEdit are interactive models. They feature an option of modifying/creating the segments by using clicks. One of the disadvantages of DeepEdit though is that it uses the whole volume to train the model. This means a bigger GPU is needed to have high-quality segmentations.
When preparing the dataset, will multiple multi-label .mrb files suffice if stored in a folder together, or is there a different format that they should be stored as?
For multi-label segmentation, you should merge all segmentations into a single file. Here you can find an example using the Total Segmentator dataset showing how you should prepare the label files for multi-label segmentation: https://youtu.be/KtPE8m0LvcQ?t=500
As part of the stored segmentations, a background segment has already been established prior to loading onto the MONAI Label module. Can that simply be added as a label when adjusting the labels of the model in the ‘configs’ folder?
If using the Segmentation model, you don’t need to specify the background label
As the seeds would have already been added when the files are loaded, and the ‘grow from seeds’ function has been initialized and applied, as these files are previously segmented, can that be submitted to the server to train the model?
Yes, you should be able to submit the segmentation to the MONAI Label model regardless of how they have been created.
When the label is ‘submitted to the server,’ how secure is that? Would the data have the potential to be accessible by an outside source in any way?
As @rbumm nicely pointed out, if you run both server and Slicer on the same PC, no data will go outside the computer. Another situation is when MONAI Label server runs on a different PC - in that case, security will depend on the type of connection you have to that PC.
I hope this helps.
Thanks again, @rbumm