Ok - the problem did sound familiar :-)
A
-----Original Message-----
From: Juergen Haenggi [mailto:[log in to unmask]]
Sent: 10 August 2006 14:41
To: 'Hammers, Alexander'
Subject: AW: [SPM] Normalization of the normalized MNI single-subject
template
Hi Alexander
you had right. The origin of the single subject template differed in y and z
coordinates!
Thans a lot
Best regards
Juergen
----------------------------------------------
Juergen Haenggi, Ph.D. student
Neuropsychology and Imaging
Division of Psychiatry Research
Psychiatric University Hospital
University of Zurich, Switzerland
P.O. Box 1931
Lenggstrasse 31, 8032 Zurich
0041 44 384 26 10 (office phone)
0041 76 445 86 84 (mobile phone)
0041 44 384 26 86 (fax)
H 115 (office room number)
[log in to unmask] (division email)
http://www.dpr.unizh.ch/ (division website)
http://www.juergenhaenggi.ch (private website)
----------------------------------------------
> -----Ursprüngliche Nachricht-----
> Von: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]] Im Auftrag von Hammers, Alexander
> Gesendet: Donnerstag, 10. August 2006 12:13
> An: [log in to unmask]
> Betreff: Re: [SPM] Normalization of the normalized MNI
> single-subject template
>
> Hi Juergen,
>
>
> Well, in the _final_ image they would be identical, because
> the normalised one will acquire the origin from the template
> you used. I was thinking more along the lines of the images
> to be normalised having differing origins.
>
> Have you checked that?
>
> Good luck, A
>
> -----Original Message-----
> From: Juergen Haenggi [mailto:[log in to unmask]]
> Sent: 10 August 2006 11:08
> To: 'Hammers, Alexander'
> Subject: AW: [SPM] Normalization of the normalized MNI
> single-subject template
>
>
> Hi Alexander
>
> Thanks for your answer. I have already checked the origins.
> They are OK. For both images the origin is at voxel
> 91/127/73 and both have the same dimensions (181/217/181).
> Therefore I guess that normalize/segment an already
> normalized image could have introduced that shift. But until
> now, I could not find the native (unnormalized) MNI single
> subject template.
>
> Best regards
> Juergen
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask]]
> > Im Auftrag von Hammers, Alexander
> > Gesendet: Donnerstag, 10. August 2006 11:48
> > An: [log in to unmask]
> > Betreff: Re: [SPM] Normalization of the normalized MNI
> single-subject
> > template
> >
> > Dear Juergen,
> >
> >
> > I haven't quite followed all the steps in your analysis but
> a 25mm y
> > and a 10mm z shift sounds like you have combined images where the
> > "origin" (~AC) was set with images where this was not the
> case. Some
> > non-SPM software will not recognize the spm origin fields and,
> > whenever you save an image in that software, will replace
> the origin
> > values with zeros, causing SPM to assume the origin in the
> centre of
> > the image.
> >
> > You can check origins with DISPLAY in any SPM version;
> should you need
> > to manually set them then you could do that with in-house
> software or
> > SPM99, the last version with a dearly missed HDR EDIT button......
> > (hint, hint)
> >
> > Good luck,
> > A
> >
> > -----Original Message-----
> > From: SPM (Statistical Parametric Mapping)
> > [mailto:[log in to unmask]]On Behalf Of Juergen Haenggi
> > Sent: 10 August 2006 07:50
> > To: [log in to unmask]
> > Subject: [SPM] Normalization of the normalized MNI single-subject
> > template
> >
> >
> > Dear SPM users
> >
> > I have run VBM5 toolbox on my subjects in order to get GM segments.
> > Now I would like to apply the masks from the MARINA software to get
> > the volumes of the masked GM structures.
> > To do that, I have also run VBM5 on the MNI single subject template
> > (Colin27) in order to
> > match the MNI single subject template (from where the masks are
> > derived) with the ICBM 452
> > T1 template (that is used in VBM5). Then I applied the
> > normalization/segmentation parameters
> > (_seg_sn.mat) to the masks (using Derormations function). So far so
> > good.
> >
> > But if I overlay the masks on the GM segments, there is a
> large shift
> > of the masks about 25mm in y-direction (too much
> > posterior) and a smaller shift in z-direction of about 10mm
> (too much
> > superior).
> >
> > The question is:
> >
> > Could it be that this shift is introduced because I have
> > normalized/segmented an already normalized image?
> > Has someone encountred similar problems?
> >
> > Thanks a lot for any suggestions.
> > Best regards
> > Juergen
> >
> > ----------------------------------------------
> > Juergen Haenggi, Ph.D. student
> > Neuropsychology and Imaging
> > Division of Psychiatry Research
> > Psychiatric University Hospital
> > University of Zurich, Switzerland
> > P.O. Box 1931
> > Lenggstrasse 31, 8032 Zurich
> > 0041 44 384 26 10 (office phone)
> > 0041 76 445 86 84 (mobile phone)
> > 0041 44 384 26 86 (fax)
> > H 115 (office room number)
> > [log in to unmask] (division email)
> > http://www.dpr.unizh.ch/ (division website)
> > http://www.juergenhaenggi.ch (private website)
> > ----------------------------------------------
> >
> >
>
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