examples in nifti format?

[tli3]

Hello, I am trying my own PET image with a tumor mask image both in nifti format using PyRadiomics. When I run the following script in python, " ... params = os.path.join(dataDir, "examples", "exampleSettings", "Params.yaml") extractor = featureextractor.RadiomicsFeaturesExtractor(params) result = extractor.execute(imageName, maskName) " it turns out that result=[] is empty. but I've tried your example nrrd files which work successfully. I wonder do PyRadiomics support the .nii.gz format? is there some requirement for the header files of the nifti? do you have some examples in that format? Many thanks.

[JoostJM]

PyRadiomics should be able to parse the niftii format (It can basically take anything that can be read by SimpleITK, with the additional constraint that it is a 3D grayscale image and mask with integer, not float, values).

I don't know what's causing your empty result, but most likely something is causing PyRadiomics to abort the extraction. If you re-run the extraction with logging enabled, the cause of your error will most likely be logged by PyRadiomics.

[ihnorton]

related question I happened across: https://stackoverflow.com/questions/50845524/medical-imaging-pyradiomics-with-nii-gz-files

[fedorov]

NIFTI should work as fine as NRRD, or any other ITK readable format. The problem is due to something else. If you can share the dataset or log we can investigate.

[JoostJM]

I agree with @fedorov. If I'm correct, PyRadiomics should print out an error message detailing why it is not working. Seeing as it's NIFTII, it is possible there is some issue with direction/origin (same problem as in the post @ihnorton mentioned)

[ihnorton]

Not my question guys, just came across it on stackoverflow 😃

[mcgoughlin]

I came across this issue, of trying to extract radiomic features from .nii.gz image/mask file types. The issue was routed in SimpleITK's inability to read the files (Error could be sourced happened to line 378 of featureextractor.py):

mask = sitk.ReadImage(MaskFilePath)

To make a very long story short, this error happened due to the NIFTI file type - I had saved my NIFTI files using the NIFTI2 image protocol (specifically, using nibabel's Nifti2Image function). At the time of writing this message, SimpleITK can only read in .nii.gz files of the NITFI1 protocol - thus, I fixed this problem by iterating through each .nii.gz file and converting them from NIFTI2 to NIFTI1. This fixed my issues completely, and pyradiomics could perform its magic perfectly well afterwards :)

I hope this helps someone!