Ensure consistent NIfTI header information

Double setting of qform to avoid header pixdim inconsistencies. This change prevents potential issues arising from subsequent image edits, ensuring reliability in image resampling processes.

totalspineseg/utils/resample.py

@@ -241,6 +241,11 @@ def resample(
     output_image_data = subject.image.data.numpy()[0, ...].astype(np.float64)
 
     output_image = nib.Nifti1Image(output_image_data, subject.image.affine, image.header)
+    # Set qform twice to ensure consistent header information
+    # This addresses an issue where the second call to set_qform may alter output_image.header['pixdim']
+    # Applying it here prevents inconsistencies that could arise from later image edits
+    output_image.set_qform(output_image.affine)
+    output_image.set_qform(output_image.affine)
 
     return output_image