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primakov / precision-medicine-toolbox

Precision medicine toolbox
BSD 3-Clause "New" or "Revised" License
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Problems with NRRD saving and loading #17

Closed strixy16 closed 10 months ago

strixy16 commented 1 year ago

I'm trying to follow along with the imaging module jupyter notebook under examples with my own dataset. I can make it up to the DICOM to NRRD conversion. When running this step,

data_dcms.convert_to_nrrd(export_path, 'gtv')

the output I get indicates that it ran successfully, but there are no new files created in the export path. I get no error messages either.

I tried converting the images to NRRDs myself to see if I could continue, but when trying to load them, I get an error saying no nrrd data is found.

This is what I tried to run image

And this is the output when I look for nrrd files in that same directory image

lavrovaliz commented 1 year ago

Hi, indeed, there is a bug in code at teh moment, so the data will not be converted if you do not have an rtstruct file... To proceed with your own files, images should comtain 'img' in name, and masks 'mask' if you are using default settings.

strixy16 commented 1 year ago

Okay I'll try changing the file names for the loading.

I do have an RTSTRUCT file included in the data when trying to save it out though.