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I am currently using nibabel 5.3.2. I wrote a script to makes an edit to an mgz image. After running the script I noticed that nibabel adds what looks like rounding error to some of the mgz header. Below is my whole script.
importnibabelasnbimportnumpyasnpimportsysoldfilledmgz=nb.freesurfer.mghformat.load(sys.argv[1])newfilledmgz=nb.freesurfer.mghformat.load(sys.argv[2])WMmgz=nb.freesurfer.mghformat.load(sys.argv[3])oldfilled=np.asanyarray(oldfilledmgz.dataobj)newfilled=np.asanyarray(newfilledmgz.dataobj)WM=np.asanyarray(WMmgz.dataobj)ifnotnp.equal(oldfilled,newfilled):WM[(oldfilled==0)& ((newfilled==127)| (newfilled==255)) ]=255WM[(newfilled==0)& ((oldfilled==127)| (oldfilled==255)) ]=1WMnew=nb.freesurfer.mghformat.MGHImage(WM,WMmgz.affine,header=WMmgz)WMnew.set_filename(sys.argv[3])nb.save(WMnew,sys.argv[3])
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