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The smoothing procedure is described in the Hutton et al paper "Voxel-based cortical thickness measurements in MRI": The spatially normalised VBCT maps were smoothed using a three-dimensional Gaussian smoothing kernel with FWHM = 3 mm. A smoothing kernel of this size was chosen to reflect the average thickness of the cortex and to account for any small discrepancies in spatial normalisation. Gaussian smoothing slightly reduces the values in the VBCT maps because it performs a weighted averaging over all voxels included by the Gaussian kernel and the values of some of those voxels are zero if they do not consist of grey matter. This effect was corrected for by dividing the smoothed VBCT maps by a binary mask of each VBCT map which has had the same smoothing applied. Essentially, it involves tissue-weighted smoothing as described in this presentation (except the presentation describes it for WM instead of GM): http://www.fil.ion.ucl.ac.uk/~john/misc/VBQ.pptx Best regards, -John On 1 November 2013 16:10, shahrzad kharabian <[log in to unmask]>wrote: > Dear list experts, > From the Dartle tools I have used the "normalise to MNI" routine to > normalize the images created by VBCT toolbox (cortical thickness and gray > matter boundary images in subject's T1_weighted space). > The images (cortical thickness map and the gray matter boundary for each > subject) overlap at subject space (before normalisation to MNI) > (figure:100percent_overlap_gmboundary_ORANGE_and_ct_GRAY_before_normalization.jpg) > but after bringing them to MNI space > (figure:overlap_swgmboundary_ORANGE_and_swct_GRAY.jpg ) they do not overlap > any more. (gm_boudary seems to be normalized well to MNI but not the > cortical thickness map which is much bigger than the MNI template after > normalization) (I have used all default options of Dartel to MNI , and have > used "No modulation" option) > Does anyone has any suggestion why it becomes like this? > bests, > Shahrzad >