I am crossposting from the Slicer forums as there has been no answer there yet, maybe someone here ran in a similar issue:
Hello, I am havong an issue on PyRadiomics 2.2.0 using the terminal (Ubuntu 18.04) for batch extraction.
I have images and masks in .nii.gz format, both with 1x1x3 mm voxels. I
have drawn bidimensional ROIs on ITKSnap with 10x10x1 dimensions, which
translate to 10x10x3 mm. Unfortunately some ROIs are also drawn on
different planes (e.g. 10x1x10 mm).
When extracting I tried to use force2D: true to enable shape2D features
and true bidimensional extraction, only when paired with 1x1x1
resampling the process fails due to the ROI not having a z value of 1
anymore (e.g. after resampling it becomes 10x10x3). Reading the docs, it
states that resampling in one of the planes should be left as 0 to keep
original dimensions and only perform in-plane resampling which I
suspect would solve my issue.
I am not able to get the extraction to work, could someone give a
parameter file example for the relevant settings to allow correct 2D
extraction in a similar situation?