RF: Adjust matrix correctly (again) for >3D images. Adjust pixdims of higher

dimensions

fsl/scripts/resample_image.py

@@ -196,6 +196,19 @@ def main(argv=None):
         xform = None
 
     resampled = fslimage.Image(resampled, xform=xform, header=hdr)
+
+    # Adjust the pixdims of the
+    # higher dimensions if they
+    # have been resampled
+    if len(resampled.shape) > 3:
+
+        oldPixdim = args.input.pixdim[3:]
+        oldShape  = args.input.shape[ 3:]
+        newShape  = resampled .shape[ 3:]
+
+        for i, (p, o, n) in enumerate(zip(oldPixdim, oldShape, newShape), 4):
+            resampled.header['pixdim'][i] = p * o / n
+
     resampled.save(args.output)
 
     return 0

fsl/utils/image/resample.py

@@ -210,7 +210,12 @@ def resample(image,
     # might not return a 4x4 matrix, so we
     # make sure it is valid.
     if matrix.shape != (4, 4):
-        matrix = np.vstack((matrix[:3, :4], [0, 0, 0, 1]))
+        rotmat         = matrix[:3, :3]
+        offsets        = matrix[:3, -1]
+        matrix         = np.eye(4)
+        matrix[:3, :3] = rotmat
+        matrix[:3, -1] = offsets
+
     matrix = transform.concat(image.voxToWorldMat, matrix)
 
     return data, matrix