Saving transformed label map for radiomics analysis

Operating system: MacOs 10.13
Slicer version: 4.8.1


So I had a label map (which was made by drawing ROI in the editor module–> call it LabelMap1), which then I transformed it using transform module then apply it using the Resample Image module to produced a transformed labelmap (call it Labelmap2).
I chose the output as Labelmap volume hoping that it will just work like previously when I use them in Radiomics (standalone).

However, I am not sure why if I put in the LabelMap2 as mask to the Radiomics, it just did not give any results, but when I enter the LabelMap1 (drawn from editor module) to the Radiomics, it works just fine.

Is there any difference in the output or way to export it? I would really appreciate any hints or any help on this. Thank you very much in advance!

Scalar and labelmap volumes are saved exactly the same way. When you load a volume, you can specify in “Add data” dialog to load the volume is a labelmap; or you can change the volume type later (in Volumes module).

Thank you very much for the fast response.
I know that we could do this, however, if we load the labelmap1 (the one that drawn in editor module), slicer will directly know that it is a labelmap, however, the labelmap2 (the one I transformed and saved as labelmap), slicer will directly load it as volumes rather than labelmap. Because I run the radiomics outside slicer, so I cannot change the volume type later on. So, I was just wondering if I could just save it with the same settings as the Labelmap1 with just some transformations.

I am sorry if the questions might not be too clear, please let me know if I need to explain more. Thank you. :slight_smile:

There may be some heuristics that try to set the default loading format correctly (e.g., if the filename ends with “-label” then loads it as labelmap by default), but scalar and labelmap volumes are otherwise saved exactly the same way.

Do you compute radiomics features using Slicer, but from command-line (without using graphical user interface)? Or a completely different software?

yepp… I compute the radiomics not using Slicer, but use Mac Terminal.

I just try to run it to radiomics in slicer, it doesn’t seem to work too. It did not give any output (such as table).

I am very confused, what I did is just transform (which is translate the mask to the right side), however, it ended up not being able to run in radiomics.

Any tips in solving this problem please? Thank you

Which package are you using? SlicerRadiomics / PyRadiomics?
Can you share an (anonymized) copy of the image and the labelmap that is not working?