Hey,
I want to indicate to my python code if a Nifti image is an image or a segmentation.
To accomplish that I want to store a single attribute in the Nifti header in one of the more flexible Nifti header fields such as a specific int in the intent_code field or a specific string in the intent_name field or the ITK_FileNotes field.
However, as it turns out SimpleITK deduces the header fields from the image data and is not so flexible in modifying specific header fields. See here: [Python] Nifti metadata cannot be modified · Issue #2177 · SimpleITK/SimpleITK · GitHub
For example in this code, I can modify the header in memory, but all changes are ignored when saving the image as Nifti. So this code does not solve my problem:
import SimpleITK as sitk
load_filepath = "image.nii.gz"
save_filepath = "new_image.nii.gz"
print("Load image...")
image_sitk = sitk.ReadImage(load_filepath)
# Change some header fields
print("intent_code: ", image_sitk.GetMetaData("intent_code"))
print("ITK_FileNotes: ", image_sitk.GetMetaData("ITK_FileNotes"))
print("pixdim[1]: ", image_sitk.GetMetaData("pixdim[1]"))
image_sitk.SetMetaData("intent_code", "1002")
image_sitk.SetMetaData("ITK_FileNotes", "Test")
# Save the image (All header modifications are ignored by SimpleITK)
sitk.WriteImage(image_sitk, save_filepath)
# New image will have only unmodified header
print("Load new image...")
image_sitk = sitk.ReadImage(save_filepath)
print("intent_code: ", image_sitk.GetMetaData("intent_code"))
print("ITK_FileNotes: ", image_sitk.GetMetaData("ITK_FileNotes"))
Are there any Nifti header fields that I can modify with SimpleITK or is there some other way to indicate in the header that the image is a segmentation?
Best,
Karol