Adapt voxel spacing of segments after changing voxel dimension of master volume

Operating system: Win10
Slicer version: 5.2.1 r31317 / 77da381


I am encountering the following problem:

  • segments were obtained by using the segment editor
  • the voxel spacing of the master volume was: 1 x 1 x 1 mm³ (the default value)
  • now I would need to change the voxel spacing of the master volume and also the voxel spacing of the
    already obtained segments

Unfortunately I couldn´t find a smooth solution for this task; once the voxel dimensions of the master volume are changed, the change of the “link”: source geometry - segmentation (in segment editor) causes the dimension of the segmentation to increase.

Intuitively I expected that a change of the master volume from 1 x 1 x 1 → 0.25 x 0.25 x 0.25 mm³ and subsequent changing the segmentation from 1 x 1 x 1 → 0.25 x 0.25 x 0.25 mm³ would cause no change in dimension of the segmentation; instead the voxel number of the segmentation is increased by 4 (1 → 0.25) in each dimension.

What is the right way to change / adapt the voxel spacing of the segments and the corresponding master volume?



The right way is to set/check the spacing of the master volume prior to segmentation avoid exactly this situation. Data spacing should be correctly set for everything downstream to work correctly.

You can fix it manually by:

  1. Right click on your existing segmentation and export it as a labelmap,
  2. Use the Volumes module to edit it in the way you did with master volume,
  3. right click the labelmap after changing the image header properties and export it again segmentation.
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