Hi, I have a question about using color lookup tables. I wanted to display an atlas nifti file WHS_SD_rat_atlas_v3.nii.gz in its original colors according to WHS_SD_rat_atlas_v3.label . I converted the lookup table to a Slicer lookup table and imported it: [image] I changed the lookup table of t…

Can you share the Slicer color file that you generated? If you want 1:1 mapping then you need to set the scalar range to match the number of colors. By the way, if you load a labelmap volume, then I think the color table is used as is - there is no intensity mapping. Have you created a script that…

[image] lassoan: Can you share the Slicer color file that you generated? If you want 1:1 mapping then you need to set the scalar range to match the number of colors. Sure - it can be downloaded from here . This version contains entries for the missing color indices in the original file, as I w…

You can import a labelmap stored in a nifti file as described here: https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentations.html?highlight=labelmap#import-an-existing-segmentation-from-volume-file You can also convert a scalar volume to labelmap volume after you loaded it, by usin…

Oh, thanks for this information - especially the first option is very nice. Additionally to having the segments available, it would be very advantageous to be able to also import colors and labels for the segments. This way, the atlas representation would be complete. Unfortunately, the initial que…

One more tip: If you work with hundreds of segments then you must use Slicer-4.11, as it has huge performance improvements for managing such large segmentations. It also has search and filter to make it easy to select a subset of segments that you are working on. Right-click on the segment list and …

Question about color lookup tables

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Question about color lookup tables

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