Dear Neeraj, dear Alle,
in SPM5, no .mat files should be created - except if you store some extra
data with the images (like e.g. diffusion information). Then, the .mat
files still do not store spatial transformations, they are stored in the
.hdr or .nii files themselves. However, programs that are not aware
of NIfTI extensions to analyze format will still not display images in
correct orientation.
Volkmar
On Tue, 7 Nov 2006, Alle Meije Wink wrote:
> Dear Neeraj,
>
> I guess that the w* files you refer to are Analyze files? Then the reason is
> probably that in NifTI files, there is always a co-ordinate transform to put
> images in an `aligned' space. After nowmalisation, this should be MNI space.
> In Analyze files there is no way to do this, that is why an extra .mat file is
> necessary.
>
> I am not really keen om .mat files either, because (as you say) they only have
> a meaning inside MatLab. The best way to not have to use them is to use NifTI
> files.
>
> atb
> Alle Meije Wink
>
> Neeraj Mahajan wrote:
> > I was using SPM2 till now, in it when I did normalization of PET images,
> > the
> > output w* files didn't have .mat files associated with them. So I could
> > use
> > the generated normalized files with some other software that understood
> > Analyze format but didn't understand .mat files.
> >
> > But with SPM5, I found that after normalization, .mat files are also
> > generated for the w* files. If I open the old normalized file (i.e. the
> > one
> > generated using SPM2) and the new normalized file in SPM5, the origin is
> > set
> > to same position. But if I open these two images in the other software,
> > that
> > doesn't understand .mat, I find that origin for them is not the same.
> >
> > Is there any option in SPM5 that would control the generation of .mat
> > files?
> > Or is there a way in SPM5 by which I can load the normalized image (along
> > with its .mat transformations) and write an image that actually has the
> > transformations applied to it. This would enable me to use the normalized
> > file with other softwares.
>
>
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
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