Skip to content

Output soft lesion segmentation #86

@valosekj

Description

@valosekj

SCIseg currently outputs binary lesion segmentation. This might not be always ideal. For example, the tissue bridges are usually computed on soft lesion segmentations (manually created using JIM). @jcohenadad thus suggested extending SCIseg inference to output the soft segmentation using dropout and Monte Carlo. After some investigation with @naga-karthik, this could be done by commenting out this line in the nnunet source code (which disable Dropout by default whenever .eval() is run) and modifying the following lines in the plans.json file:

"dropout_op": torch.nn.Dropout,
"dropout _op_kwargs": 0.5,

EDIT: clarified why that line has to be commented out

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions