Gabriel,

> Thanks for your answer, As a matter of fact I have check these on SPM,
> with the same images I have perform cross-sectional analyses using
> either SPM8 and VBM8, so there ir no problem with the images in this
> sense

OK, if orientation is fine, this leaves the origin to check. As I said, 
try the reset origin option in vbm8 and see how you fare. You could also 
try coregistering the images (not reslice) prior to submitting them to 
vbm8, but I have not tried this.

> About the acquisition part, yes, unfortunately they were acquired like
> this. Do you think that there is no way to compare in a longitudinal
> way? do you have any ideas on how to proceed in this case?

Well, the problem is: whatever you report as being due to differences in 
time, an astute reviewer is going to have to ask you "how can you prove 
these differences are not due to the differences in image acquisition". 
And I don't see how you have an answer to that question as your sequence 
difference is perfectly correlated with the difference you are 
interested in. If you had some acquired this way and some another way, 
you could conceivably use acquisition scheme (or voxel size or so) as a 
covariate, but here, I see no easy way out. In fact, right now I see 
none, but I have not thought about this long enough (and don't know your 
dataset well enough) to wreck your project off-handedly.

Good luck,
Marko


>  > Date: Tue, 28 Jan 2014 16:24:31 +0100
>  > From: [log in to unmask]
>  > To: [log in to unmask]; [log in to unmask]
>  > Subject: Re: [SPM] longitudinal VBM8 for non-MRI nada
>  >
>  > 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/
>  > ____________________________________________________
>  >

-- 
____________________________________________________
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/
____________________________________________________