I am working with nii files (head MRI scans) that i 1)open and save in 3D Slicer as nii.gz 2)Load the nii.gz file with python and take a certain number of slices from the 3D numpy array (for example the 10 slices from the axial view). 3)Then I construct a nii image to save using the saved original nii affine transformation data. However after saving it isn’t properly displayed if I load the resliced nii file into Slicer. The whole code basically looks like this:
image = nib.load(file_name_MRI) original_image_affine = image.affine image = image.get_data() resliced = image[:,60:70,:] resliced_nii_image = nib.Nifti1Image(resliced, original_img_affine) nib.save(resliced_nii_image, path_to_save_destination)
So my question is how can I save the resliced nii image (what affine data should I use when saving) in the way that it is correctly/ displayed in 3D Slicer?
Thanks in advance!