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/
____________________________________________________
|