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I would suggest only realigning the data that you plan to use. I have copy/pasted some of the online help that may explain what you observed... Because of subject motion, different images are likely to have different patterns of zeros from where it was not possible to sample data. With masking enabled, the program searches through the whole time series looking for voxels which need to be sampled from outside the original images. Where this occurs, that voxel is set to zero for the whole set of images (unless the image format can represent NaN, in which case NaNs are used where possible). Best regards, -John On Friday 21 November 2008 14:12, Julia Weiler wrote: > Dear SPMers, > > 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. > > Any advice would be aprreciated. > > Thanks > > Julia > > > Julia Weiler > > Ruhr-University Bochum > Inst. of Cognitive Neuroscience > Department of Neuropsychology > GAFO 05/606 > Phone: +49-234-3223574 > Fax: +49-234-3214622