Hey everyone, I’m labeling brain segments in MONAILabel.
The masks / ROIs used as input for Monailabel are a subselection extracted by slicerio.extract_segments() function from a 3DSlicer Segmentation node.
I modified the config files from the models DeepEdit and Segmentation (from the radiology app) to match our masks, but I haven’t made much progress so far.
Here is a screenshot of the DeepEdit config file
I’ve included 5 masks so far, which are clearly identified in 3D Slicer (see figure below):
In 3D Slicer, the 5 labels are separate and clearly identified
However, when I open them in MONAI Label, the labels often get collapsed. For example, the ipsilateral and contralateral hemisphere labels may collapse into the contralateral hemisphere, the cerebellum and lateral ventricles become one label, and some labels are completely absent (see figure below):
In Monailabel, all 5 labels are collapsed into 3 - cerebellum, ipsilateral and contralateral lateral ventricles
Has anyone encountered this issue before or have any advice on how to fix it?