Dear Henna,
> For a region of interest based fMRI study we are attempting to align our
> functional and anatomical images (using the functional image closest to the
> image of the short anatomy as a reference) with SPM5. The difficulty is that
> while our anatomical image covers the whole brain, the functional images only
> cover a portion of the left hemisphere and were taken at a different ‘angle‘. In
> other words, the orientation of the slices in the functional and anatomical
> images is different, so the alignment fails.
>
> Is SPM5 capable of realigning functional volumes when these volumes are
> partial? And if yes, how can this be done?
I guess, you mean coregistration instead of realignment, isn't it? Realignment of these scans, i.e. movement correction, should work in any case I presume.
You could try the following:
You should align manually the anatomical scan and the functional scan with the display tool, i.e. orient your functional scans in the way that the orientation is somewhat similar to the anatomical scan. You can do that by specifying the pitch, roll and yaw angle in terms of pi (i.e. writing in 'pi' or 3.1416 rotates the image by 180 degree). You can do that for one functional scan and then press 'reorient images' and select all functional scans you have to rotate in the same way.
So, you do not have to do it for each scan separately. When all subjects were scaned in approximately the same orientation, you can try to apply it also for them.
This will give the coregistration a much better starting point and then it might work ...
An alternative (in case you are still collecting data): Run one single scan with the same orientation but more slices an use that for the coregistration and aplly the parameter to your functional scans.
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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