Gabriel,
just my 2 cents:
> I have defined the origin in all my scans to the AC.
Have you verified that the images conform to the orientation standard
that spm expects? I.e., do they look as a template does when you load
them in spm (i.e., coronal [top left], saggital looking left [top
right], axial with r=r [bottom]) ? Have you tried normalizing the images
using unified segment in spm?
> As a second step I
> notice that my images have different matrix sizes, i.e. voxel size of
> 1.2x0.9x0.9, matrix = 135x256x256; and the follow-up scans have voxels
> of 1.2x0.8x0.8, matrix = 120x188x188. For which I decided to reslice the
> image so to increase the matrix of the second one. I'm sending you a
> picture with an example before and after (attached image with the three
> MRIs).
If you really acquired all your timepoint 1 images in one way, and all
timepoint 2 images in another way, then this, I am afraid, is a very
serious problem. Even if you reslice the images (which is probably not a
good idea as it introduces additional interpolation effects), they will
still be acquired in two different ways, which means that it is not
possible to disambiguate effects of time from those of sequence difference.
> When I started the longitudinal VBM, it works till the "Coarse affine
> Registration" when the error prompts, when I open the images they appear
> to be rotated and their origin has been changed, see attached image with
> the two MRIs.
This usually only happens when the original image orientation and/or
origin setting is unreasonably (to spm :) far off the expected
orientation. I would suggest verifying spm can handle the images in the
first place, and perhaps using the "set origin using center of mass"
option in vbm8.
Good luck,
Marko
--
____________________________________________________
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
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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