I am facing this problem while saving/exporting the segmentation into a binary label map. The problem is with HEART only. The heart contains multiple substructures. When I am saving the whole Heart and multiple substructures, the whole heart is showing some empty spaces. The empty spaces mainly contain the substructures. I am getting below image of whole heart:
When I select all the substructures of heart then I am getting the below result:
I want whole heart should look like the below image without detailed information of substructures. Ignore the texts in it.
To create a segment that is the union of all other segments, you can use Logical operators effect’s Fill option, with setting Editable region → Inside all segments.
@lassoan Thanks for your suggestion. I tried “Hollow” option. It is giving me the result but other structures are also impacting. Most probably I am not selecting correct parameter. Could you please suggest correct parameter settings?
“Hollow” effect changes a solid structure into a hollow structure. Based on what you described, this is not what you need.
Have you tried to use the “Logical operators” effect as I described above? If you want to keep other segments unchanged then set “Allow overlap” in Masking section.
Thanks for sharing the video. My Slicer package is stable version and up to date. I tried in Mac and Linux but there is no change in result. Here is the latest outcome.
Could you try it on a sample data set, creating the segmentation from scratch, to see if there is something special about your segmentation? Or save your scene as a .mrb file, upload it somewhere, and post the link here, so that I can try to reproduce the behavior on my computer?
I’ve uploaded the sample data and corresponding segmentation file. Please use this link https://easyupload.io/0klfow to download those files. The problem is with only “Whole Heart”. I have attached few screenshots for your reference. The problem is arising when I am saving the segmentation into labelmap.
Thank you, by loading the linked file I was able to reproduce the unexpected behavior. There was a bug in Logical operator effect and so the mask was only applied if you performed some editing operation (e.g., use the Paint effect) before.
I’ve submitted a fix, so tomorrow’s Slicer Preview Release will not have this issue. As a workaround, use Paint effect to draw a small scribble somewhere (you can undo it or erase it right after it) and then use the Logical operators effect.
Note: Do not save segmentations in Nifti files. They are intended for brain images only and have many issues and limitations. For example they cannot store overlapping segments.
Thanks so much! This version has partially solved my issue. I want the effect will only be applied to the “whole heart”, not to other organs. For example, I am unable to detach esophagus from whole heart.
Thanks so much! I tried that option too and there is no improvements on the issue.
Here, I attached the screenshot. I created segment 9 for applying logical operation. You can see all other segments are not visible. segment 9 contains all the organs. I just want heart will display here.
My goal is to FILL the empty regions inside the heart. For example, I am showing the empty regions of heart.
