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This example shows how to estimate fat, muscle, and bone volume in a CT image by simple thresholding.
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# Download a sample data set (chest CT) | |
import SampleData | |
masterVolumeNode = SampleData.SampleDataLogic().downloadCTChest() | |
# Create segmentation | |
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode") | |
segmentationNode.CreateDefaultDisplayNodes() # only needed for display | |
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode) | |
# Create temporary segment editor to get access to effects | |
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget() | |
segmentEditorWidget.setMRMLScene(slicer.mrmlScene) | |
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode") | |
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode) | |
segmentEditorWidget.setSegmentationNode(segmentationNode) | |
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode) | |
# Create segments by thresholding | |
segmentsFromHounsfieldUnits = [ | |
["fat", -200, -50], | |
["muscle", 25, 70], | |
["bone", 130, 3000] ] | |
for segmentName, thresholdMin, thresholdMax in segmentsFromHounsfieldUnits: | |
# Create segment | |
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment(segmentName) | |
segmentEditorNode.SetSelectedSegmentID(addedSegmentID) | |
# Fill by thresholding | |
segmentEditorWidget.setActiveEffectByName("Threshold") | |
effect = segmentEditorWidget.activeEffect() | |
effect.setParameter("MinimumThreshold",str(thresholdMin)) | |
effect.setParameter("MaximumThreshold",str(thresholdMax)) | |
effect.self().onApply() | |
# Delete temporary segment editor | |
segmentEditorWidget = None | |
slicer.mrmlScene.RemoveNode(segmentEditorNode) | |
# Compute segment volumes | |
resultsTableNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLTableNode') | |
import SegmentStatistics | |
segStatLogic = SegmentStatistics.SegmentStatisticsLogic() | |
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID()) | |
segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID()) | |
segStatLogic.getParameterNode().SetParameter("LabelmapSegmentStatisticsPlugin.enabled","False") | |
segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled","False") | |
segStatLogic.getParameterNode().SetParameter("ScalarVolumeSegmentStatisticsPlugin.volume_mm3.enabled","False") | |
segStatLogic.computeStatistics() | |
segStatLogic.exportToTable(resultsTableNode) | |
segStatLogic.showTable(resultsTableNode) | |
# Export segmentation to a labelmap | |
labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode') | |
slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(segmentationNode, labelmapVolumeNode, masterVolumeNode) | |
slicer.util.saveNode(labelmapVolumeNode, "c:/tmp/BodyComposition-label.nrrd") |
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