Hi Jürgen,
not exactly sure I wholly understood what you did but could it be that
for what you have in mind
> 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.
[...]
> Then I applied the normalization/segmentation parameters
> (_seg_sn.mat) to the masks (using Derormations function).
you may actually want to use the INVERSE spatial normalization
parameters? If I got your approach right, you want to assess your masks
in native space, in which case you have to apply the seg_inv_sn.mat-file
to the masks in MNI-space.
> Could it be that this shift is introduced because I have
> normalized/segmented an already normalized image?
I do not think so: although spm does use some starting estimates as to
the affine registration, I doubt it would mess up the registration that
much. Also, this would be easy to check by segmenting Colin27 again with
the affine registration in spm5's segmenting options switched off.
Best,
Marko
--
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Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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