bug: predicted mask file is not completely aligned to the ground truth

[strixy16]

In the saving of the predicted mask, only partial alignment is completed:

medsam2-inference/inference.py

Lines 285 to 288 in 4ee259d

	# Save mask
	save_mask = sitk.GetImageFromArray(segs_3D)
	save_mask.SetSpacing(spacing)
	sitk.WriteImage(save_mask, masks_dir / f"{patient_id}.nii.gz")

The spacing is one part, but the origin needs to be copied over as well, or else the images won't overlay in a display (like in 3DSlicer)

To add:

origin = image.GetOrigin()
save_mask.SetOrigin(origin)

We also have a function for this in readii, so alternatively could use:

from readii.image_processing import alignImages

save_mask = alignImages(image, save_mask)