Hello Jelle,
the issue ist that realignment will "only" correct for orientation
differences in the header and will not by default write the images. This
makes sense in the classical context of realign, normalize, smooth, as
these corrections will be taken into account when normalizing. If you
want to do your analyses in native space (for which, in my humble
opinion, there are good reasons) then you will need to reslice the
images, as in "realign & reslice". This should fix it.
Cheers,
Marko
Jelle Demanet wrote:
> Hello all,
> We have a question regarding preprocessing and using non-normalised images in a first-level analysis. I have done the pre-processing with only the first three steps (co-registration, slice timing and realignment). However, our first level script that we use still does not seem to agree with this. It says there's a problem with the orientations, apparently the images do not all have same orientation and/or voxel sizes. Anybody had a similar problem and knows how to solve it?
>
> Kindest Regards,
> Jelle
>
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PD 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
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http://www.medizin.uni-tuebingen.de/kinder/epn/
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