As you are observing, it is important to check that the imported image stack has the correct image spacing as the first step of your workflow. Since everything else (segmentations → models → measurements) are all dependent on this piece of information. This is especially true if you importing these images from 2D formats like PNG/TIFF etc which doesn’t preserve this information.
You don’t have to redo the segmentation but it will take you a few steps to get them in correct alignment. This is what I would suggest (@lassoan is there a simpler fix?)
- Go to
segmentationsmodule export your current segmentation as a label map - After the export right-click on the exported labelmap and choose “Edit Properties”
- This will take you
Volumesmodule where you can cross reference the slice spacing, dimensions, and IJK matrix of the master volume and this labelmap. Expand the Volume Information tab (see below). Everything reported for the labelmap should match to that of the master volume. You can use the dropdown button to switch between the original volume and the labelmap. (see below) - Once the labelmap is fixed, you can right click and choose “Convert to labelmap to segmentation”.
This new segmentation should have the right spacing, Delete everything else…
Next time, you’d help yourself if you use the ImageStacks from SlicerMorph extension and then enter the correct spacing in the module and then import the stack.
