Closed Mathematinho closed 5 years ago
@Mathematinho,
That notebook represents a very old version of PyRadiomics (check the output, it containts the version: 1.0-post17)
As to the enabled settings, that variable is now called settings
, similarly, enabled filters is now enabledImagetypes
. Enabled features/classes are still in enabledFeatures
.
Finally, setting force2D=True
does not automatically switch your shape features to 2D, it is intended to deal with voxel anisotropy (by ignoring offsets in the slice direction, requiring only isotropic size in-plane).
For extracting in 2D (single slice, including 2D shape features): disable class shape
and enable class shape2D
, set force2D=True
. Note that this only works if your segmentation also represents just 1 slice.
Finally, the settings that were enabled are also part of the standard diagnostic features in the output: diagnostics_Configuration_Settings
thank you @JoostJM. problem solved.
Describe the bug I was trying to pass the force2D keyword arguments into pyradiomics. But it seems not making any difference in the output. I still see all the 3D shape features and don't see the 2D shape features.
i tried both hard-code and using a parameter file follow the code from https://www.radiomics.io/pyradiomicsnotebook.html
neither worked.
my guess was the parameter was not passed into featureextractor. In fact, i wasn't able to print the default settings. you can see that in the screen grab below.
Version (please complete the following information):
Thanks.