I am trying to use the python interface to load a (float) scalar volume in the form of a signed distance field want to apply thresholdscalarvolume to generate a label map with everything below 0.0. It doesn’t seem to be working in terms of creating the label map and running the cli interface. her…

You can create a segmentation from thresholded input volumeNode like this: volumeNode = ... thresholdValue = 80 # Create temporary labelmap labelVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode") slicer.vtkSlicerVolumesLogic().CreateLabelVolumeFromVolume(slicer.mrmlScene,…

You can do it much simpler way: voxelArray = slicer.util.arrayFromVolume(volumeNode) voxelArray[voxelArray < thresholdValue] = 0 slicer.util.arrayFromVolumeModified(volumeNode) Next steps depend on what you would like to do. Would you like to convert this to a segmentation node?

I figured out two things. runSync forces the command to wait until completed whereas run immediately returns and has to be checked. the second thing was checking cliNode.GetErrorText() is empty the problem is that I used lower case “below” rather than “Below”. now the line executes but doesn’t sho…

That is much simpler. thank you. yes that is it exactly, I saw the another post where there are commands to import the the label map to a segmentation mode, but hadn’t gotten that far yet.

is it possible to set the master volume in the editor? can I do from the segmentationNode? and also is it possible to select the slice views orientation button via as well?

Yes, good point, you can easily create segments directly from a grayscale volume by choosing the volume as master volume and using Threshold effect. See full examples in the script repository .

Thanks, what I am doing is a little more complicated. I am pre segmenting with vmtk and want to edit that segmentation with slicer. I used the command segmentEditorWidget.setMasterVolumeNode(volumeNode) to set the master volume but it didn’t change the gui view like it did when changed the name of…

[image] kayarre: I used the command segmentEditorWidget.setMasterVolumeNode(volumeNode) to set the master volume but it didn’t change the gui view like it did when changed the name of the segmentation. You can change view by using slicer.util.setSliceViewerLayers method . [image] kayarre: …

Whats the python command to do the alignment of the image volume and segmentation? [figure] found it: segmentEditorWidget.rotateSliceViewsToSegmentation()

when I try to execute the following I get an error: segmentEditorWidget = slicer.qMRMLSegmentEditorWidget() segmentEditorWidget.setMRMLScene(slicer.mrmlScene) segmentEditorWidget.setMRMLScene(slicer.mrmlScene) gives an error: Python console user input: segmentEditorWidget.setMRMLScene(slicer.mrml…

These errors are logged because the widget attempts to update itself but segment editor parameter node is not set yet (using setMRMLSegmentEditorNode). You can ignore these errors and we’ll update the widget to not log these errors.

Threshold scalar volume to labelmap

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Threshold scalar volume to labelmap

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