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I would guess that this is because the initial affine registration is going wrong. In SPM99, a skull stripped brain does not register very well to a template image containing all the non-brain tissue. Best regards, -John | We are looking at the inhomogeneity correction of t1 image in the | segmentation part of SPM99. Does anybody know why there is about 10% | difference in the corrected volume between using stripped (of non-brain | materials) and unstripped input? In both cases, we chose the "spatial | normalization" (input is not spatially normalized) and "a little bias" option. | The difference has some structures in it and does not appear to be due to | round off errors. | | Thanks. | | Jeih-San Liow