Dear Lea,
> I am referring to John Ashburner's comment on the Preliminaries step under
> Unified Segmentation (wikibooks). The first step on page 3, under Unified
> Segmentation, and Preliminaries, he suggests to make sure that the images
> are "reasonably well aligned with the template", using the Check Reg
> function. However, no matter what order we open the images in, the second
> batch of images is always misaligned.
I'm sorry, but that has to be like this. Check Reg shows always the other images in relation to the first one, i.e. if they are misaligned, in does not matter in which order you select them, since they are misaligned, anyway. CheckReg is mainly just a display tool.
How strong is the misalignment? "Reasonably well aligned with the template" means, they are axial, the orientation is correct (i.e. left right, anterior posterior, superior-inferior) and they are not off-center, (i.e. the origin is not too different), but they don't need (and never will) match.
Good luck,
Karsten
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Karsten Specht, PhD
Department of Biological and Medical Psychology
& National Competence Centre for functional MRI
University of Bergen
Jonas Lies vei 91
5009 Bergen
Norway
Tel.: +47-555-86279
Fax: +47-555-89872
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http://fmri.uib.no/
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