Issues with multiple labels and masks overlapping in Monailabel

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?

Start with the reported slicerio.extract_segments() output and the modified DeepEdit and Segmentation configuration files, then reproduce the label-loading behavior in MONAILabel with the five masks. Done means identifying why distinct labels are collapsed or omitted and confirming that all five labels remain separate when opened in MONAILabel.