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OMG this is a good catch. We wrestled with this a long time ago when setting up Slice Geometry. The correct way to set slice spacing (pixel spacing in z) from a DICOM is to use the slice position info (0020,1041 or 0020,0032) and divide by (stack size - 1). It can be out by not much or quite a bit.

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BoneJ

@bonej.org

A closer read of this paper makes it seem that some of the scans were done in chunks of a few slices each, and that the chunks had different slice spacing from each other. That's a bit of a mess: making a composite assuming equal z-spacing throughout the volume will lead to distortions.

27/10/25, 11:46 am0 reposts0 likes

BoneJ

@bonej.org

27 Oct 2025

Could be fixed by determining the total number of slices and start and end slice position, then calculating average slice spacing and interpolating the original image data accordingly. A bit messy. Good on 3D Slicer for detecting, alerting users and sorting it!