BF: Only FNIRT coefficient fields clobber NIFTI headers - displacement fields

are fine. Generating a slightly less incorrect (but still incorrect) v2w
affine for the former. Bug in test script

fsl/data/image.py

@@ -312,12 +312,27 @@ class Nifti(notifier.Notifier, meta.Meta):
         qform  = header.get('qform_code',  -1)
         sform  = header.get('sform_code',  -1)
 
-        if intent in (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
-                      constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
+        # FNIRT non-linear coefficient files
+        # clobber the sform/qform/intent
+        # and pixdims of the nifti header,
+        # so we can't correctly place it in
+        # the world coordinate system. See
+        # $FSLDIR/src/fnirt/fnirt_file_writer.cpp
+        # and fsl.transform.nonlinear for more
+        # details.
+        if intent in (constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
                       constants.FSL_DCT_COEFFICIENTS,
                       constants.FSL_QUADRATIC_SPLINE_COEFFICIENTS):
-            log.debug('FNIRT output image detected - using qform matrix')
-            voxToWorldMat = np.array(header.get_qform())
+
+            log.debug('FNIRT coefficient field detected - generating affine')
+
+            knotpix       =  header.get_zooms()[:3]
+            refpix        = (header.get('intent_p1', 1),
+                             header.get('intent_p2', 1),
+                             header.get('intent_p3', 1))
+            voxToWorldMat = transform.concat(
+                transform.scaleOffsetXform(refpix,  0),
+                transform.scaleOffsetXform(knotpix, 0))
 
         # If the qform or sform codes are unknown,
         # then we can't assume that the transform

tests/test_fsl_convert_x5.py → tests/test_scripts/test_fsl_convert_x5.py

@@ -43,7 +43,7 @@ def test_convert_flirt():
             ref.getAffine('fsl', 'world'),
             xform,
             src.getAffine('world', 'fsl'))
-        gotxform, gotsrc, gotref = transform.readFlirtX5('src2ref.x5')
+        gotxform, gotsrc, gotref = transform.readLinearX5('src2ref.x5')
         assert np.all(np.isclose(gotxform, expxform))
         assert src.sameSpace(gotsrc)
         assert ref.sameSpace(gotref)