Dear Marko,
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, about the oriantation conform, see the attached image, where I'm comparing in check_reg the two images of one of my subjects (upper columns) and the standard SPM T1 MNI152 and the VBM8 avg_T1_Dartel_IXI550_MNI155 templates (lower columns left and right respectively), and they match perfectly fine with the orientation. So all this part of my images is apparently the problem, at leat at this point.
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?
> 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/
> ____________________________________________________
>
> 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/
> ____________________________________________________
>