@d246a informed me, that she is not able to load the segmentation niftis provided in the dataset of the KITS challenge. The error message is:
I checked the files with a simple python script and it turned out, that the value type is 64-bit signed integer, which we do not support yet.
A quick workaround was to convert the segmentations using this script:
import os import SimpleITK as sitk root = "/home/kleina/E132-Projekte/temp_data/dtrofimova/kits2021/case_00000/segmentations" filename = 'artery_instance-1_annotation-1.nii.gz' filename_out = 'output.nii.gz' file_to_load = os.path.join(root, filename) outputImageFileName = os.path.join(root, filename_out) input_image = sitk.ReadImage(file_to_load) print(input_image.GetPixelIDTypeAsString()) cast_image = sitk.Cast(input_image, sitk.sitkInt8) sitk.WriteImage(cast_image, outputImageFileName)
A possible solution could be to add the value type to the supported ones in cmake (MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES).