Conerting RTstruct file to nrrd : Getting a meaningful result with correct dimensions?

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1

Operating system: MacOS
Slicer version: 4.9.0.-2018-08-04
Expected behavior: Produce nrrd file with 15x512x512x128 dimensions
Actual behavior: Finding nrrd file with 15x357x211x128 dimensions

Hi All,

  1. Would someone be able to post step by step instructions for converting an RTstruct file to an nrrd file?
    I am new to 3dslicer and am finding the program and its UI rather confusing. I believe screenshots would be helpful.

  2. I tried to follow the question here and I think that I did it correctly.

    image
    image2196×1374 458 KB

    However, I am getting what looks to me like a weird result because the dimensions of the nrrd coming from the rtstruct file are kind of weird.

image
image1554×990 84.1 KB

Why would I get a (15, 357, 211, 128) matrix as a result of converting the rtstruct associated with a 512x512 image series. The 15 makes sense since there are 15 structures, the 128 makes sense since there are 128 images but why is it 357x211 and not 512x512?

This dimension issue is not only not making sense to me but is also causing the size mismatch issue when I try to run pyradiomics to calculate feature on the structures.

I am new to 3dslicer and image analysis and appreciate your patience very much. I have tried other software solutions like plastimatch to do this conversion and having a difficulty with the dimensions there as well where I will get a 3x512x512x128 instead of 15x512x512x128.

I am wondering if I should try to write a script that generates nrrds from RTstruct myself. Thanks a bunch again for any help.

2

The dimensions you get are the union of the “effective extents” of your structures, i.e. the region that contains data. You can export it with any geometry if you set a reference volume in the Import/Export section of the Segmentations module.

You can also automatically do such conversion using this module in SlicerRT.