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> I'm using SPM2 to spatially normalise lesioned brains using affine only > normalisation. Is there a way to view the final cost function achieved? It is not saved anywhere, but if you really wanted to, you could modify spm_normalise.m, such that the values were saved. > > Also, if I were to apply nonlinear warping following the affine > transformation, is there a way I can check how good the affine part was? One measure could be based on the variance in the nonlinear part of the transformation by: t=load(spm_get(1,'*_sn.mat')); sum(t.Tr(:).^2) Best regards, -John -- Dr John Ashburner. Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK. tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381 fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john