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How does ANTs handle qform and sform in NIFTI 1 images?
ITK has changed its approach to NIFTI headers over time. Common to all ITK implementations is the restriction that ITK supports a rigid (rotation + translation) transform between voxel and physical coordinates. The variation in NIFTI I/O comes from changes in how ITK looks for the transform in the NIFTI header, and how it writes that information to output NIFTI files.
The main difference between ITK used in ANTs 2.3.5 and in 2.3.4 is that ITK now prefers the sform matrix to read and write the header transform. Previously, it used the qform header fields, but this suffered from precision issues in addition to being difficult to read.
On read, a rotation and translation are extracted from the sform matrix. Non-rigid scaling or shearing in the sform is not used and will not be preserved in output. When reading an image, the qform will be used if the sform is not present or has a code indicating it is not a voxel-to-physical space transform.
On write, the rotation and translation for the output image is written back into the sform and qform.
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The text below describes the previous ITK behavior, which was similar but preferred to read the qform if it was present. On output, the transform was written to the qform, and the sform was set to zeros.
ANTs uses ITK image I/O, which uses a common framework to read many different image formats. ITK supports a rotation, but not a full affine transform, to translate coordinates from index space (voxel indices) to physical space. Therefore it can only use qform when reading a NIFTI-1 image. When writing NIFTI output, only the qform is written; the sform is replaced with zeros.
The exact procedure for defining the transform to physical space is here: itkNiftiImageIO.cxx
In general, qform is used on input. The rotation comes from the quaternion, the scaling comes from the pixel dimensions, and the translation from the qoffset fields. This is NIFTI "method 2" as explained in the NIFTI-1 documentation. This is the procedure whenever the qform code is greater than 0, regardless of the sform code.
In rare cases, the qform code is 0. This should never be the case except for backwards compatibility, ie reading old ANALYZE files. If the qform code is 0, indicating no valid qform, the rotation and scaling are extracted from the sform, if it is present.
When writing NIFTI files, ITK encodes the rotation, translation and scaling in the qform. The qform code is set to 1 (NIFTI_XFORM_SCANNER_ANAT), and the sform code is set to 0. The loss of the sform is unavoidable because the ITK I/O code reads images into a common internal structure, independent of the individual image format on disk, and only supports a rigid transformation.
ITK reads and writes a variety of file formats. Images are read into a generic ITK image object, and after processing the results are written out in the desired format. As a result, there can be precision errors in the output NIFTI header.
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qform and sform codes may be interpreted differently. ITK uses qform whenever qform_code > 0.
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The sform will be overwritten in output images, and sform code will be set to 0. If the sform is not identical to the qform, information will be lost.
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Another issue: "Note that in cases where both an SForm and QForm are present, ITK gives precedence to the QForm while SPM/MRIcroGL/FSLeyes/Mango give precedence to the SForm. The rationale for the SPM approach is clear: QForms were designed to provide an idea of native space, while the SForm could provide the user an easy way to provide a starting estimate. When informed of this difference the ITK group elected to keep their method to ensure backward compatibility. To support both conventions, recent versions of SPM change both the SForm as well as QForm when the user changes the origin with the "Display" button. While the original intent of the SForm and QForm was to provide a method to encode both native scanner as well as some losslessly re-oriented coordinates, the differences in implementations supports SPM's method of using the same value for both to ensure consistent display and processing."
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In registration, the fixed image may have an sform, which will be ignored in the registration. The warped moving image will have only a qform. Thus the registration may work correctly but appear to be incorrect because of differences in how the NIFTI header is interpreted.