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AIM-Harvard / pyradiomics

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. Support: https://discourse.slicer.org/c/community/radiomics
http://pyradiomics.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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[FEAT EXTRACTION] Wavelet filtering #768

Open nadiaxf opened 2 years ago

nadiaxf commented 2 years ago

Hi all, I am pretty new to python in general and very new to pyradiomics. I am trying to run batch processing and i would like to try wavelet band-pass filtering to see if it improves my results.

I am running PyRadiomics on Mac using Terminal. This is the command I am using to run batch processing:

pyradiomics <Path/to/CSV/file/containing/Imagepaths&Maskpaths> -o <Path/to/desired/output/resultCSVfile> -f csv

Can someone please explain to me where in the above command should I specify that I would like to implement wavelet band pass filtering?

JoostJM commented 2 years ago

application of filters is done in the parameter file (styled as a yaml text file). It is passend on the commandline via the -p switch. The repository contains examples of such files, and all possible settings are explained in the online docs

When batch processing, you can add the -j <n> swicht, where <n> is the number of CPU cores you want to run in parallel.