Incorrect Header Readout from *.nrrd Images using scikit-image 0.15

NifTK / NiftyNet

[unmaintained] An open-source convolutional neural networks platform for research in medical image analysis and image-guided therapy

http://niftynet.io

Apache License 2.0

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Incorrect Header Readout from *.nrrd Images using scikit-image 0.15 #343

Open elitap opened 5 years ago

elitap commented 5 years ago

I was using the same code on two different machines, one having installed scikit-image 0.14.2 and the other 0.15. It seams that since version 0.15 scikit-image is able to read .nrrd images, however it does not correctly read the meta information, which leads to wrong image dimensions. On the other machine using scikit-image 0.14.2 the loader faild to load the .nrrd image and the next loader 'SimpleITK' was used, which could correctly load the image.

wyli commented 5 years ago

Hi @elitap I think you could add loader = simpleitk to your config's input data sections.

Also, we might change the order of the loader's attempts -- prefer simpleitk if it's installed. I'll double-check that.