Hi guys, I am trying to save some clicks and time by wrting a python script for saving my segmentations to files (labelmaps (nii.gz)) I simply do not undestand how to provide the reference image to the function: slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode() so my code is…

See code snippet that does what you need in the script repository , and a complete working example here .

thank you very much for your reply! After running this Slicer crashes down: #load volume masterVolumeNode = slicer.util.loadVolume('c:/Users/desserdmi/Desktop/data.nii.gz', returnNode=True) #make vtk object of mastervolume masterVolumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkmasterVolumeNode…

The original error was caused because that function is static, and the way you called it, it passes the object instance (self) as well. To the code you recently pasted: [image] Dmitriy_Desser: masterVolumeNode = slicer.mrmlScene.AddNewNodeByClass(“vtkmasterVolumeNode”) You don’t need this f…

Thank you very much for your reply! the reason, why I have tried this is the error message I get: Traceback (most recent call last): File "<console>", line 1, in <module> TypeError: SetReferenceImageGeometryParameterFromVolumeNode argument 1: method requires a VTK object Anyway, is there no sim…

In general, my advice is that try running the lines within the python interactor one by one, checking the content of variables. The error messages are usually pretty straightforward. For example if the message is that it should be a VTK object and it’s not, then you need to find out what it is inste…

We are of course aware that some simple segmentation software (that cannot work with arbitrary number of master volumes with varying geometry, overlapping segments, etc.) can save everything in a simple 3D labelmap. However, since Slicer is much more flexible, we need to use a more general file form…

Thank you so much guys! editing .slicerrc works perfectly! This is what I was looking for! Cheers, Dima

Hi Guys, I am trying to automate storing the segmentation Node using 3D Slicer extension. self.currentSelector = slicer.qMRMLNodeComboBox() self.currentSelector.nodeTypes = [“vtkMRMLScalarVolumeNode”] … slicer.modules.segmentations.logic().ExportVisibleSegmentsToLabelmapNode(actual_segmentation…

[image] Jithendra: The problem I am facing is I am unable to get reference to the actual Node name referred by slicer.qMRMLNodeComboBox() You can get the node selected in qMRMLNodeComboBox by calling currentNode() method. See more examples and background information in Slicer programming tuto…

Thank you @lassoan . This solves my problem. I was able to get the name using slicer.util.getNode(“currentNodeId value”).GetName()

Export segmentation to labelmap using python

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Export segmentation to labelmap using python

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