My dear radiologists saved all the segmentations they created without a reference as compressed niftis. Therefore, all the annotations appear cropped if I load them as numpy arrays using nibabel.
My image data is 240x240x192; however, when loading the images they appear with varying sizes cropped around the actual annotations.
How can I load numpy arrays from the with the proper dimensions of the reference image and in the correct location?
Probably, the necessary information is saved somewhere in the header because I can still open the images with slicer and they show up correctly.
Thanks for your help!