hi 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 …

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: [image] Output from segmentation Support If you want simpler, then you can export DICOM. Unfortunately the DICOM SEG exporter is currentl…

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…

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.

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

Support

Topic		Replies	Views
The saved segmentation file size is different from the original volume nrrd file size Support segmentation , nrrd , image-dimensions	4	1120	May 31, 2022
How to get segmentations as numpy arrays with same dimensions? Support segmentation	7	2625	June 25, 2020
Output from segmentation Support	5	4721	August 3, 2017
Segmentation size Support	1	267	September 17, 2020
Exporting a ".seg.nrrd" Segmentation with Extent of Original Image Support	1	163	September 24, 2026

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

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