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The image header for NIFTI has two separate ways to represent positional information in a viewer. Some programs (ITK-SNAP) prefer to edit the qform and others prefer to edit the sform (SPM, FSL), but these choices have evolved over the years along with what happens to the other matrix when the preferred one gets edited (set the other to 0s, match the other to the preferred, leave the other as it was). ITK-SNAP sets the sform to 0s, a potential problem for other viewers. The following tools can help: sqdiff.sh tells you whether the sform and qform of an image differ. sqdiff_wrap.sh will run sqdiff on every image it finds in subject subdirectories (sub*) of the current directory. q2s.sh copies the qform to the sform. s2q.sh copies the sform to the qform. All are based on the fsl tool fslorient.
Because the sform and qform are stored differently, they have different levels of precision. It is possible to copy the sform to the qform and still find that they are reported to be a bit different by sqdiff.sh. If you copy the qform to the sform, however, any differences will be completely removed.
sqdiff.sh compares the sform and qform. You see results if they are different. In the example above, ITK-SNAP has set the sform to 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 which is quite different that the qform!
To make the sform and qform match (a very good idea), you can run either q2s.sh or s2q.sh. After generating a mask with ITK-SNAP, you can see that the sform has been zeroed out, so we want to copy the qform to the sform: 1e1e36bf2d