Don't fail if sform/qform don't match

applywarp --usesqform will currently fail if the input or reference image qform and sforms are not equivalent to within a strict tolerance. applywarp will currently also always use the sform, regardless of the sform/qform code values. This MR removes the equivalence restriction, and changes applywarp to use the sform or qform, depending on their codes.

There is no reason for a tool to require that the sform and qform affines are identical. All tools should follow the standard FSL convention of using sform if sform code !=0, or qform if qform code !=0, or a fall back scaling affine.

applywarp.cc

@@ -526,15 +526,13 @@ float ApplyWarpHelper::hist_mode(vector<float>  vec)
 }
 
 NEWMAT::Matrix ApplyWarpHelper::get_and_confirm_s_qform(const NEWIMAGE::volume<float>& vol,
-							const std::string&             fname)
+                                                        const std::string&             fname)
 {
-  NEWMAT::Matrix sform = vol.sform_mat();
-  NEWMAT::Matrix qform = vol.qform_mat();
-  if ((sform - qform).NormFrobenius() > 1e-6) {
-    cerr << "sform and qform not identical in image " << fname << endl;
-    exit(EXIT_FAILURE);
+  if ((vol.sform_code() + vol.qform_code()) == 0) {
+    std::cerr << "sform/qform codes are unknown - using scaling matrix (" << fname << ")" << std::endl;
   }
-  return(sform);
+
+  return vol.newimagevox2mm_mat();
 }
 
 // This ought to be really simple, but because of the peculiarities of apply_warp it must