Why are my segmentations being saved as only the bounding box size rather than the size of the original image?

I have made a large amount of segmentations on 3D slicer but when I try to save them they are only the size of the area covered by the segmentation. For example if the segmentation covers 100x40x40 slices it only saves the slices covered rather than the size of the original image. I want to use it as a mask so this is causing issues. I have tried saving straight fromt he segmentation editor as a seg.nrrd file and through the segmentation module by exporting it as a label map. how do I fix this?

You need to specify a Reference volume if you want a larger extent in your saved file.

See these topics that answer the same question:

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Also note that in recent Slicer Preview Releases we save the entire segmentation region by default (crop to segmented region is an option in Save data dialog). This way, more memory and disk space is used but the saved file is compatible with software that rely on having exact match of image extents with the master volume.


Thank you, since I am on a work laptop I can’t use preview releases at the moment but I will keep it in mind if I get the chance to change.

Thank you. I didn’t realise there was another reference volume section in the advanced part of the segmentations module. I was relying on the segmentation editor master geometry.

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4 posts were split to a new topic: How to get segmentations as numpy arrays with same dimensions?