Hi, I’ve been reading the threads about naming/numbering and the colormaps for segmentations: Export Segmentation as Labeled LabelMap Copying segment names/colors from one segmentation to another I am not sure to be able to export the labels according to the colortable properly: similar to @appa…

[image] jhlegarreta: I made sure that I am using exactly the names in my colortable, and have simplified it t As I wrote above, you need to use the color names that show up in Colors module, which is not exactly what is stored internally in the color table file (due to spaces are replaced by …

Sharing the color table and a labelmap/segmentation would probably help. Without those it is hard to tell what you might be doing wrong or missing.

[image] jhlegarreta: I am manually segmenting structures e.g. 29 and 35. When exporting them, if I pick the colortable that I am using, they are numbered as 37, 38 (besides the background, 0), which I would say is not expected already. @lassoan I can replicate this behavior on latest stable. …

Thanks for the quick reply @muratmaga . Sharing the color table and a labelmap/segmentation would probably help. Without those it is hard to tell what you might be doing wrong or missing. You’re right. Not ideal to try to guess without data, but I chose not upload the data somewhere due to variou…

I’ve tested Slicer-5.6.2 and everything works well: if a segment name matches a color name in the chosen table, then the label value in the exported labelmap volume is the color index. What confused @muratmaga was that internally in color table files, space character is stored as underscore (probab…

Thanks for giving this a try @lassoan . I made sure that I am using exactly the names in my colortable, and have simplified it to the following: # Color table file my_colortable.txt # 4 values 0 Background 0 0 0 0 1 Left 231 255 0 255 2 Right 111 231 0 255 3 New_I_name 0 230 92 255 4 Another_I_New_…

[image] jhlegarreta: I made sure that I am using exactly the names in my colortable, and have simplified it to the following: I confirm that everything works as expected (i.e., labelmaps are exported with correct indices) when you replace underscore (_) with space. I tested it 5.6.2. If 5.2.2…

OK, thanks Andrass. Thanks Murat as well for the valuable input. you need to use the color names that show up in Colors module, which is not exactly what is stored internally in the color table file (due to spaces are replaced by underscores). Indeed, underscores are replaced by whitespaces, and…

Exporting a segmentation paired to a custom colortable

Support

Topic		Replies	Views
Preserve colors from segment editor node and export it as Nifti LabelMap Support segmentation , nifti , file-export , labelmap	8	623	December 1, 2023
Segmentation terminology to labelmap indices Support segmentation , segment	2	229	January 23, 2023
Add Segment to SegmentationNode uses invalid color values (scalar) and adds a new colortable node Support segmentation , python , custom-color-table	5	53	January 3, 2026
Incorrect values when converting segmentation to binary labelmap Support	20	209	June 3, 2025
Export Segmentation as Labeled LabelMap Support	17	3850	May 12, 2023

Exporting a segmentation paired to a custom colortable

Related topics