NaN values during 3D feature extraction

[pavi1303]

I was extracting the 3D collage features for my volume and mask file which are in .nii format. I created a collage object with this mask and image, declared a haralick window size of 3 and then called the execute function. But, the variable (collage_output) had NaN values for both dominant angles. I'll share my files with you shortly via email. It would be great if you could look into this.

[nathanhillyer]

@pavi1303 How were you running collage? In our docker container or in a python file?

[nathanhillyer]

Also, which version of collageradiomics do you have running (if being run outside of docker).

[pavi1303]

I am running it as a python file. I declared use_3D as True and then created a collage object with my mask, image and used a haralick window size of 3. Then called the collage execute function. I'm currently using the version 0.3.3. I installed them via the pip module.

[nathanhillyer]

@pavi1303 Apologies for the delay, I was put out of commission by the storms in Texas. I will be able to communicate promptly now.

When I try those files I see data in the masked region, e.g. at collage_output[238,117,103], for example. In the non-masked areas I see NaN values. Are you seeing the same on your end?