BF: Can't short-cut convertDeformationType, as it causes inf recursion between

DefField.deformationType and detectDeformationType. Also fix applyDeformation
where not using altref

fsl/transform/nonlinear.py

@@ -582,9 +582,6 @@ def convertDeformationType(field, defType=None):
         if field.deformationType == 'absolute': defType = 'relative'
         else:                                   defType = 'absolute'
 
-    if field.deformationType == defType:
-        return field.data
-
     # Regardless of the conversion direction,
     # we need the coordinates of every voxel
     # in the reference coordinate system.
@@ -743,6 +740,9 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
                                              mode='constant',
                                              cval=-1)[0]
 
+    else:
+        field = field.data
+
     field = field.transpose((3, 0, 1, 2))
     return ndinterp.map_coordinates(image.data,
                                     field,

fsl/utils/image/resample.py

@@ -67,7 +67,9 @@ def resampleToReference(image, reference, matrix=None, **kwargs):
         newShape = newShape + oldShape[len(newShape):]
 
     # Align the two images together
-    # via their vox-to-world affines.
+    # via their vox-to-world affines,
+    # and the world-to-world affine
+    # if provided
     matrix = affine.concat(image.worldToVoxMat,
                            affine.invert(matrix),
                            reference.voxToWorldMat)