Hi, I have been working in python on a new deep learning algorithm. I would like to use Slicer to display the output to evaluate, but I am not sure how to import the output npz files into slicer for display, nor how to convert it into a SimpleITK image for proper orientation in Slicer and create a m…

You can set voxels in a volume node from numpy array by calling updateVolumeFromArray .

How do I import the npz file in the first place though? When I drag and drop or direct the data import to the files, it doesn’t import anything.

Also, I’m assuming this method correct the spacing in the normal simpleITK way? Where z,x,y get converted to x,y,z dimensions?

You can load npz file into a numpy array using standard numpy commands (numpy.load). If you load plain numpy arrays then you need to store metadata (such as origin, spacing, axis directions) before numpy array conversion, then retrieve it when needed. This may become easier in the future (see this d…

I don’t understand. I looked at the documentation, but how do yoy store the metadata information to convert?

Also, is there a way to import .nii.gz files into slicer?

[image] stevenagl12: I don’t understand. I looked at the documentation, but how do yoy store the metadata information to convert? If you load an image (nrrd, nift, etc.) then you have all the basic metadata. If you decide to convert to numpy then it is your responsibility to store the metadat…

I have the metadata information from the original files, but when I convert them to numpy/tensor and back for pytorch, I would like to import them into slicer. So if I call in the file with np.load, and then use the updateVolumeFromArray command, how can I add the metadata to get the appropriate ima…

You can set origin, spacing, axis directions on the MRML volume node that you created from the numpy array.

I have loaded in my numpy arrays, but when I go to run the updateVolumeFromArray, I am getting the error AttributeError: ‘numpy.ndarray’ object has no attribute ‘GetImageData’. I have tried to change it to a SimpleITK image, and this is not working either.

Importing Numpy & NPZ files into Slicer

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Importing Numpy & NPZ files into Slicer

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