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Dear Marko, You're right; coregistration had failed. i checked registration for my subjects, but not for both halves of the experiment, which evidently I should have. >We used to do this manually by centering and orienting the brain along the anterior-posterior commissure line, and you can still do that (depending on how many subject you have). I actually did this manually for all my subjects, although I think I made a mistake for this one -- the anatomical image is off center. I have to look back at the original image and figure out where the problem arose. >perhaps also within session (particularly if subjects moved around in between acquisitions). I have coregistered all my subjects, but I didn't consider the possibility of doing it within session. Within session is perhaps overkill, but there would be a pretty strong argument for within "half" -- it was between the first and second half of the experiment that the subjects got out and moved around. Thanks for your help! I know how to proceed now. Best, Katie On Mon, Sep 26, 2016 at 2:27 AM, Marko Wilke < [log in to unmask]> wrote: > Hello Katie, > > this is so drastic a failure that it points to the initial affine > registration having failed. To fix this, you should make sure the subjects > brains are in rough alignment with the template, and with each other. > > We used to do this manually by centering and orienting the brain along the > anterior-posterior commissure line, and you can still do that (depending on > how many subject you have). If you have a lot, I would rather suggest you > try using a combination of coregistration, and potentially re-setting the > origin to the center of mass (there is a function in the vbm8 toolbox, if I > remember correctly). > > Also, make sure you always coregister anatomical and functional images > from each subject, perhaps also within session (particularly if subjects > moved around in between acquisitions). > > Hope this helps > Cheers > Marko > > > Katie Surrence wrote: > >> >> Dear SPM experts, >> >> I was missing half the brain at the second level, and I've tracked the >> problem down to a subject for whom DARTEL normalization has apparently >> failed, though only for the second half of the experiment. >> (Participants got out of the scanner and walked around between halves, >> so some settings may have changed.) It fails by squashing the brain >> down in the bottom half of the field of view. >> >> My question is, okay, I know what the problem is, now what? Try another >> kind of normalization and see if it does better, report that I did so in >> any resulting paper, and give that participant its own "different >> normalization" regressor at the second level? Exclude data for the >> problematic half of the participant? Or is there a way to fix this? >> >> I am attaching two pictures, one of the unsmoothed normalization failure >> and one of the smoothed. The brains are centered in the field of view >> until the normalization step. >> >> Thanks for any help you can provide! >> >> Best, >> Katie >> > > -- > ____________________________________________________ > Prof. Dr. med. Marko Wilke > Facharzt für Kinder- und Jugendmedizin > Leiter, Experimentelle Pädiatrische Neurobildgebung > Universitäts-Kinderklinik > Abt. III (Neuropädiatrie) > > Marko Wilke, MD, PhD > Pediatrician > Head, Experimental Pediatric Neuroimaging > University Children's Hospital > Dept. III (Pediatric Neurology) > > Hoppe-Seyler-Str. 1 > D - 72076 Tübingen, Germany > Tel. +49 7071 29-83416 > Fax +49 7071 29-5473 > [log in to unmask] > > http://www.medizin.uni-tuebingen.de/kinder/epn/ > ____________________________________________________ > >