Dear Volmar,
One thing I observed is that if I rename the .mat file and display the image
in SPM5 then the origin is same as when the .mat file is in place. If I read
the image in SPM2 without the .mat file then the origin is not the same but
with the .mat file SPM2 properly reads the image and the origin is same as
in case of SPM5.
So from this observation and your reply, is it correct to say that in case
of NIfTI format, there is some extra data written (in addition to the
Analyze data) because of which SPM5 can read the image correctly even in
absence of .mat. SPM2 can read the image correctly in presence of .mat file
because it reads only the non-NifTI extra info and then uses the .mat file
to correctly interpret the image.
Also, what I am doing is taking a PET image, setting the origin, normalizing
and co-registering the image (with help of MRI and template images). The
.mat file is generated when I change the origin and then it exists for
normalized as well as co-registered image.
Other than these steps I am not doing anything else.
Regards,
Neeraj
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of Volkmar Glauche
Sent: Wednesday, November 08, 2006 3:05 AM
To: [log in to unmask]
Subject: Re: [SPM] Avoid .mat files after normalization
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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