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> We had a methodology question about the VBM procedure of Goode et al. We > are at the point where we apply the warps to whole brain images, followed > by segmentation. > > Is it valid to apply the .mat files obtained from the gray matter images to > whole brain images, segment, and then do statistics on gray and white > matter maps? The spatial normalisation of grey matter should be much improved by processing the data in this way. White matter spatial normalisation should be improved in part, except for around the ventricles. Spatially normalising based on grey matter should mean that the grey/white interface is aligned. > Put another way, is it valid methodology to apply statistics > to white matter maps normalized with the gray matter image to gray matter > template normalization parameters ? I am not actually that keen on VBM on white matter, for reasons that I have previously mentioned on the list. Much more smoothing is needed in order to achieve the partial voluming effect that is necessary for VBM to give meaningful results. > Or would it be better to normalize the > whole brains separately, using the parameters from the gray matter image to > gray matter template warp, and the white matter image to white matter > template warp, and then segment the normalized images, and use use the gray > and white matter maps derived from the warps of the same tissue type? Or > does it even matter? Each method is likely to give slightly different results (but I can't say for certain as I haven't done any comparisons). The most appropriate way of doing things is likely to involve modifying the spatial normalisation routines so that grey matter is matched with grey, and white with white simultaneously. 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