Hello,
looks like I started this, so...
> I am having exactly the same problem as you! I am scanning rats and some
> of them managed to rotate around slowly during the scan - when I run my
> preprocessing (realign, reslice only mean image, coreg mean to
> structural and then normalise and segment to template) I find that the
> functional scans are still rotated round by the end of the scan.
I am still under the impression that, if you use spm to display your
images, you should see a difference in the orientation after realignment
(potentially play around with voxel and world space, but it should be
visible). It may not be that obvious but one way to find out whether
anything happened at all to the images is to check the timestamp of
their last modification (that is one reason why I still like img/hdr
combination, you can tell much easier :)
Also, what I meant is when doing "coreg mean to structural", you have to
specify all other EPI images from this run as "other" images. This is
where I have repeatedly failed to do the obvious myself, hence my
warning to check that this actually happened. Again, time of header
modification is one way to be sure.
> you, I tried to use reorient to put the functional scans roughly in
> alignment , but when I ran realign etc again the motion curves were
> identical as if I had not reoriented the images and they were all still
> rotated by the end.
Not sure this is correct but theoretically, if you rotate all images in
one run in an identical way, the difference between them, and what it
needs to register them on top of each other, will not change. This would
be one explanation, another could be that the realignment procedure uses
the original orientation which may still be encoded in the header somewhere.
> One suggestion I had was to use cogregister to put the functional in
> alignment - but this did not work.
You mean you ran coreg, estimate on all images individually, with image
1 as the reference? That should work, albeit it seems a bit cumbersome
and may not be as good as simple realignment as it is mainly meant for
between-modality matching.
> The only thing that worked was to run my preprocessing twice. But is
> this a good idea? I have no idea, I only know that now my scans line up
> nicely. Could someone tell me why running realign etc twice is not a
> good idea?
If you do not reslice, my only concern would be that it should not be
necessary, and that I would rather like to know where the underlying
problem is.
Not sure this helps but I think I am going to leave it at that.
Cheers,
Marko
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PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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http://www.medizin.uni-tuebingen.de/kinder/epn/
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