Exporting multiple segmentations into individual binary labelmaps?

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1

I have a project where we segmented 500 tumors from 50 patients and into a single segmentation with 1 segment per tumor.

I want to generate a probability map by adding all 500 lesions into a binary file, then divide it by the number of subjects.

Is there a way to bulk export every segment to a binary labelmap with a value of 1 (or 0)?
Or alternatively is there a way to bulk add segments into a single layer without overlaps but summed intensity values?

Do I have to use python interactor for this?

THanks in advance!

2

You could look into the Batch Processing module in the SlicerRT extension.

3

Thanks Csaba! It doesn’t seem to work on Mac. The solution was to export each segmentation layer individually (which was tedious but doable with only 6 layers.

  1. I turned on show Segment layer on the Segment viewer
  2. Exported each layer’s segments to a separate binary label map
  3. SimpleITK filters was used to binarize them (0 vs. 1)
  4. Added binary maps to each other
  5. Converted the summed map to a FLOAT (Cast Scalar module)
  6. Divided by the number of patients (created a labelmap whose entire value was the equivalent of the number of patients using BinaryImage Threshold filter in Simple ITK filters)
  7. Voila the result is a population lesion probability map.