Dangerous change - scaleOffsetXform and transform.transform were

returning/assuming transposed affines (column-major). This is because that's
what OpenGL uses.

fsl/data/atlases.py

@@ -495,7 +495,7 @@ class AtlasDescription(object):
         # Load the appropriate transformation matrix
         # and transform all those voxel coordinates
         # into world coordinates
-        coords = transform.transform(coords, self.xforms[0].T)
+        coords = transform.transform(coords, self.xforms[0])
 
         # Update the coordinates 
         # in our label objects
@@ -594,7 +594,7 @@ class LabelAtlas(Atlas):
         location, or ``None`` if the location is out of bounds.
         """
 
-        voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
+        voxelLoc = transform.transform([worldLoc], self.worldToVoxMat)[0]
         voxelLoc = [int(v) for v in voxelLoc.round()]
 
         if voxelLoc[0] <  0             or \
@@ -642,7 +642,7 @@ class ProbabilisticAtlas(Atlas):
                   location. Returns an empty list if the given
                   location is out of bounds.
         """
-        voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
+        voxelLoc = transform.transform([worldLoc], self.worldToVoxMat)[0]
         voxelLoc = [int(v) for v in voxelLoc.round()]
 
         if voxelLoc[0] <  0             or \

fsl/data/featanalysis.py

@@ -355,7 +355,7 @@ def loadClusterResults(featdir, settings, contrast):
         # later on.
         coordXform = fslimage.Image(
             getDataFile(featdir),
-            loadData=False).worldToVoxMat.T
+            loadData=False).worldToVoxMat
 
         if not op.exists(clusterFile):
             return None

fsl/utils/transform.py

@@ -73,9 +73,9 @@ def scaleOffsetXform(scales, offsets):
     xform[1, 1] = scales[1]
     xform[2, 2] = scales[2]
 
-    xform[3, 0] = offsets[0]
-    xform[3, 1] = offsets[1]
-    xform[3, 2] = offsets[2]
+    xform[0, 3] = offsets[0]
+    xform[1, 3] = offsets[1]
+    xform[2, 3] = offsets[2]
 
     return xform
 
@@ -337,8 +337,8 @@ def transform(p, xform, axes=None):
               scalings.
     """
 
-    p = _fillPoints(p, axes)
-    t = np.dot(xform[:3, :3].T, p.T).T  + xform[3, :3]
+    p  = _fillPoints(p, axes)
+    t  = np.dot(xform[:3, :3], p.T).T + xform[:3, 3]
 
     if axes is not None:
         t = t[:, axes]