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
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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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