Hello everyone, I want to extract HU values at each voxel from my CT scan files, which for I use the following command: HU_Array = slicer.util.array(‘myfile.nrrd’) However, using “nrrd” file I get the values at all voxels. I was wondering if there is a way that I can extract values in a specific area after segmenting? Thank you, Zahra

Run either the maskvolume or Split Volume effect with your segmentaiton and then run your one liner. MaskVolume will set all voxels out of segmentation are to 0 (or your value of your choosing). While SplitVolume will crop out everything outside of the segmentation area.

Thank you @muratmaga for your reply. Do you know how I can get " the coordinates of voxels" inside a specific segmentation, instead of the whole nrrd file?

If you mean the physical (RAS) coordinates, I think you can rework this example: [image] Convert between RAS and numpy array indices Development First, download MRHead data from Sample Data module import numpy as np volumeArray = slicer.util.array("MRHead") # Get the image data in numpy array format volumeArray[60, 127, 150] = 0 # Make one voxel black, numpy array is in KJI, not IJK. volumeNode = slicer.mrmlScene.GetFirstNodeByName("MRHead") volumeNode.Modified() # I think this is needed to let Slicer know the image was modified. ijkToRasMatrix = vtk.vtkMatrix4x4() volumeNode.GetIJKToRASMatrix(ijkToRasMatrix) ijkPoint = np.array([150…

Thank you @muratmaga for your help.

If you want to know the coordinates of all voxels with a specific value you can work from this example: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#get-the-values-of-all-voxels-for-a-label-value

That’s very useful, I appreciate that.

Extract values at voxels within a segment

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muratmaga (Murat Maga) March 15, 2023, 4:35am 5

If you mean the physical (RAS) coordinates, I think you can rework this example:

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Extract values at voxels within a segment

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