As reported by Romain
" This seems to be to do with the fact that only the image on which a segmentation has been performed have a non-zero segmentation image when OK-ing the Segmentation manager window. I think the problem then stems down to the default behaviour of a non-segmented image (all 0 or all 1). It is currently set to define an empty segmentation image for non-segmented image.
This can be circumvented by selecting the whole image as the segmentation image for these. But it would make more sense to me if it was the opposite (non-segmented image are fully kept), as this would be more easily compatible with the intensity threshold."
As reported by Romain " This seems to be to do with the fact that only the image on which a segmentation has been performed have a non-zero segmentation image when OK-ing the Segmentation manager window. I think the problem then stems down to the default behaviour of a non-segmented image (all 0 or all 1). It is currently set to define an empty segmentation image for non-segmented image. This can be circumvented by selecting the whole image as the segmentation image for these. But it would make more sense to me if it was the opposite (non-segmented image are fully kept), as this would be more easily compatible with the intensity threshold."