Field coil inhomogeneities cause intensity gradients across the scan image which is does not effect analysis by a radiologist, but throws a threshold right out. This causes a different threshold to be needed in different parts of the dataset (different slices can be noticeably brighter or darker), and causes gradients across a given slice.
This figure illustrates the effect of an intensity gradient A
histogram was taken of each half of the brain and the grey-white border
was chosen as the trough between the grey and white peaks. The red
contours were chosen using this method for the left side of the image
and the contours in yellow were chosen using the right half of the
image. The red contours are consistently inside the yellow contours
(the grey-white threshold was chosen to be a higher intensity using the
left side of the image.