Create labelmap segmentations from a nifti mask file

index.ts

// load the mask file as a volume

const maskUrl = 'mask-url'
const imageIds = await createNiftiImageIdsAndCacheMetadata({
  url: maskUrl,
})

const maskVolumeId = 'mask-volume-nifti'
const maskVolume = await volumeLoader.createAndCacheVolume(maskVolumeId, {
  imageIds,
})
maskVolume.load()

// create a segmentation, refering to the mask volume

const segmentationId = 'nifti_segmentation'
const segVolume = await volumeLoader.createAndCacheDerivedLabelmapVolume(
  maskVolume,
  {
    volumeId: segmentationId,
  }
)

await cornerstoneTools.segmentation.addSegmentations([
  {
    segmentationId,
    representation: {
      type: SegmentationRepresentations.Labelmap,
      data: {
        volumeId: segmentationId,
      },
    },
  },
])

// iterate over the voxels of nifti volume and add non-zero values to the segmentation

let i = 0
while (1) {
  if (i === maskVolume.numVoxels) {
    break
  }

  const value = maskVolume.voxelManager.getAtIndex(i)
  if (value !== 0) {
    segVolume.voxelManager.setAtIndex(i, value)
  }
  ++i
}

await segmentation.addSegmentationRepresentations(viewportIds, [
  {
    segmentationId,
    type: SegmentationRepresentations.Labelmap,
  },
])