BF: Use 'pixdim' affine for scaled voxel display space, not 'pixdim-flip', as

the latter will potentially L/R flip some images

fsleyes/displaycontext/displaycontext.py

@@ -185,7 +185,7 @@ class DisplayContext(props.SyncableHasProperties):
        system, with origin set to the centre of voxel ``(0, 0, 0)``, and
        voxels scaled by image pixdims. This is accomplished by setting the
        :attr:`.NiftiOpts.transform` property for every ``Nifti`` overlay to
-       ``pixdim-flip``.
+       ``pixdim``.
 
     3. **Reference image** space
 
@@ -533,7 +533,10 @@ class DisplayContext(props.SyncableHasProperties):
         # (reference image), we decide based on the ref
         # image.
         elif space == 'scaledVoxel':
-            space = self.getSelectedOverlay()
+            space    = self.getSelectedOverlay()
+            srcSpace = 'pixdim'
+        else:
+            srcSpace = 'pixdim-flip'
 
         # Use the FSL / FLIRT convention - if the affine
         # determinant is negative, assume neurological
@@ -542,7 +545,7 @@ class DisplayContext(props.SyncableHasProperties):
             ref = self.getOpts(space).referenceImage
             if ref is not None:
                 opts  = self.getOpts(space)
-                xform = opts.getTransform('pixdim-flip', 'display')
+                xform = opts.getTransform(srcSpace, 'display')
                 return npla.det(xform) > 0
 
         # no nifti overlays loaded
@@ -901,7 +904,7 @@ class DisplayContext(props.SyncableHasProperties):
         # listener on the bounds property.
         with props.skip(opts, 'bounds', self.__name, ignoreInvalid=True):
             if   space == 'world':       opts.transform = 'affine'
-            elif space == 'scaledVoxel': opts.transform = 'pixdim-flip'
+            elif space == 'scaledVoxel': opts.transform = 'pixdim'
             elif image is space:         opts.transform = 'pixdim-flip'
             else:                        opts.transform = 'reference'
 
@@ -1168,7 +1171,7 @@ class DisplayContext(props.SyncableHasProperties):
 
         if self.displaySpace == 'scaledVoxel':
             ref      = self.getSelectedOverlay()
-            srcSpace = 'pixdim-flip'
+            srcSpace = 'pixdim'
         else:
             ref      = self.displaySpace
             srcSpace = 'display'

fsleyes/displaycontext/niftiopts.py

@@ -36,7 +36,8 @@ in one of several ways:
                                 image appears to be stored in neurological
                                 order, the X (left-right) axis is
                                 inverted. The origin is fixed at the centre of
-                                voxel ``(0, 0, 0)``.
+                                voxel ``(0, 0, 0)`` (or ``(X-1, 0, 0)`` for
+                                 inverted images).
 
  **world**                      (a.k.a. ``affine``) The image data voxel
                                 coordinates are transformed by the
@@ -445,7 +446,7 @@ class NiftiOpts(fsldisplay.DisplayOpts):
         if ds == 'world':
             voxToRefMat = voxToWorldMat
         elif ds == 'scaledVoxel':
-            voxToRefMat = voxToPixFlipMat
+            voxToRefMat = voxToPixdimMat
         elif ds is self.overlay:
             voxToRefMat = voxToPixFlipMat
         else: