Dear Michelle,
Just to be sure (as the Clinical Toolbox outputs a considerable amount of files), you are talking about the anatomical file prefixed with 'w' and the lesion file prefixed with 'bws'?
Normally the Clinical Toolbox indeed would apply the same transformation parameters to both the anatomical scan and the lesion map and as such the anatomical file prefixed with 'w' and the lesion file prefixed with 'bws' should align after normalisation (provided of course they aligned before normalisation).
Perhaps you could send a screenshot illustrating the problem?
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