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 …

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 ima…

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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