Merge pull request #41 from mu40/voxsize-from-affine

Compute resolution from affine to fix voxel-size bug.
freesurfer · Oct 9, 2024 · 041905f · 041905f
2 parents c80a3de + c2daf2e
commit 041905f
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/surfa/image/framed.py b/surfa/image/framed.py
@@ -474,9 +474,6 @@ def reorient(self, orientation, copy=True):
         world_axes_trg = get_world_axes(trg_matrix[:self.basedim, :self.basedim])
         world_axes_src = get_world_axes(src_matrix[:self.basedim, :self.basedim])
 
-        voxsize = np.asarray(self.geom.voxsize)
-        voxsize = voxsize[world_axes_src][world_axes_trg]
-
         # initialize new
         data = self.data.copy()
         affine = self.geom.vox2world.matrix.copy()
@@ -497,6 +494,9 @@ def reorient(self, orientation, copy=True):
                 affine[:, i] = - affine[:, i]
                 affine[:3, 3] = affine[:3, 3] - affine[:3, i] * (data.shape[i] - 1)
 
+        # derive new voxel size
+        voxsize = np.sqrt(np.sum(affine[:self.basedim, :self.basedim] ** 2, axis=0))
+
         # update geometry
         target_geom = ImageGeometry(
             shape=data.shape[:3],