Registering T1 image with AAL atlas intensity values changes

I performed following steps

  1. register T1 image to MNI space and compute the transformation matrix
  2. then take the inverse of that matrix
  3. apply registration using inverse matrix to AAL atlas and tranform it into my subject space (T1 space)
  4. now i am overlapping mask (tumor mask) with this atlas based image
    tumor mask has three different labels. but in AAL atlas space intensity values has been changed so how i can get three different ROI based on tumor mask?

I suspect you need to use nearest neighbour interpolation in step 3. (-interp nearest option for mrtransform).

I tried it by using nn interpolation too. but the result is same.