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John, once again, thanks for your helpful answers. > I think this is probably because spm_defaults has not been run. > When spm starts up, it runs spm_defaults.m, which loads a bunch of > default settings as global variables. If you just call spm_sn3d > from the command line, then you may not have all these defaults > loaded into memory. I thought so, too, but even if I first start spm and then run the command in the matlab window, it does not work. Could that be because I disabled Java (matlab -nojvm) ? I can' check right now since I am running something lenghty... > It is supposed to do this. After it has estimated the spatial > normalisation parameters, it writes out a spatially normalised > version of the image that the parameters were estimated from. > This image is used for quality control, and it is displayed in > the orthogonal viewer next to the template image. Right, this is what got me confused - it looks like it is done and writes out an image with the adequate size, and then (when you think you are finally through), it starts writing stuff out all over again. But if you say that's fine, who am I to doubt ;) I just wanted to be sure it's okay, since it costs me a lot of time. Thanks for your help. Marko -- =============================================== Marko Wilke, MD Research Fellow, Imaging Research Center Children's Hospital Medical Center Cincinnati [log in to unmask]