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Dear List, I have a question with regard to the thickness study using VBCT toolbox. I am trying to create the Thickness map the way it is described in the Documentation, but I ma coming to some difficulties as following: - I have created the ct maps and the gm_boundry maps in subject space. When overlapping them in volume space (fslview) they completely overlap on top of each other. And I find it good! - then I made the Dartel templates using the Dartel toolbox, and the Template_6 seems reasonable. Also, the warp field were made. - Then, I" Apply DARTEL warp fields to VBCT maps" and seems here something goes wrong: Because now when I overlap the smoothed warped to MNI gm_boundary and cortical thickness (swct*.nii) maps, although the image sizes are similar, the cortical thickness map is obviously more stretched than the swgm_boundary map (and even overlapping on another template in MNI, the swct* maps are more stretched) . So, now overlapping them on top of each other gives me a very thin boundary of the cortex which is covered by the swgm_boundary image and the swgm_boundary do not show the boundary of the cortical thickness map any more. So I am wondering what has gone wrong here? the problem is that I wanted to use the swgm_boundary map to restrict my statistics to the mask of gm_boundary which is similar in all subjects, but with this situation it makes no sense. I will be very thankful to get any suggestions from you! Shahrzad