Hi,

I have some 7T-T1 datasets that I would like to process with FreeSurfer. However, regardless of whether I use the complete or the skull-stripped volumes as input, the Talairach normalization fails (in both cases the standard brain appears smaller than the individual brain when opened with tkregister2). The reason seems to be that the skull is dark in these volumes while its bright in the template. FSL flirt seems to work properly, so I would like to know whether there is any chance of replacing the talairach.xfm files with the output from this normalization?

Any ideas are very much appreciated! Thanks a lot!

Sebastian