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I found the solution of this problem : the function spm_reslice adds some NaN values when normalizing an image. When you reuse the function spm_affreg afterwards with these resliced images, the function spm_sample_vol doesn't like the NaN values, for a reason that I cannot explain because this function is private. Nevertheless, an "easy" solution is to write a line after each spm_sample_vol calls that changes the NaN of the output of the function into 0. Example : intially : line 135 of spm_affreg : [F,dF1,dF2,dF3]=spm_sample_vol(VF(1),y1,y2,y3,1); After modif : [F,dF1,dF2,dF3]=spm_sample_vol(VF(1),y1,y2,y3,1); F(isnan(F))=0;dF1(isnan(dF1))=0;etc... Hope it will help some of you. Best, Christopher Coello