Dear Julia,
> After realignment, the lower portion of the brain was missing in all
> volumes, whether acquired late or early during the experiments (see bottom panels
> in the attached picture. left: early scan; right: late scan).
> I tried both options "Register to first" and "Register to mean", but the
> results were the same.
>
> Due to the large movements, I may not be able to use the data of this
> late experimental phase anyway. However, I would like to understand,
> why the lower brain portion is missing in all volumes after realignment.
> I would have expected that this is only the case in the late volumes, where
> it was missing from the beginning on.
SPM5 resamples only those voxel which are present in ALL volumes, which makes sense, since you can estimate your statistic also only for those voxels which are present in all scans.
So, even thought writing the images after realignment (or normalisation) for the whole brain (if present) would not help, since latest in the statistic, you will loose these voxels.
So, I would strongly recommend to exclude that subject (or at least to cut the session, where the movement occurred), since all your following SPM analyses will be without the temporal lobe.
Good luck,
Karsten
> I encountered a problem during preprocessing of my fMRI data using SPM5.
> One of the subjects showed large movements (up to 4cm) during the last
> quarter of the experiment. Due to that, the late scans did not cover the
> whole
> brain anymore (temporal lobe missing; see attached picture: the top panels
> show an early scan on the left, a late scan on the right.)
>
> After realignment, the lower portion of the brain was missing in all
> volumes,
> whether acquired late or early during the experiments (see bottom panels
> in the attached picture. left: early scan; right: late scan).
> I tried both options "Register to first" and "Register to mean", but the
> results
> were the same.
>
> Due to the large movements, I may not be able to use the data of this
> late experimental phase anyway. However, I would like to understand,
> why the lower brain portion is missing in all volumes after realignment.
> I would have expected that this is only the case in the late volumes, where
> it was missing from the beginning on.
--
-------------------------------------------------------------
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
[log in to unmask]
http://fmri.uib.no/
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