This may be caused by the motion correction. SPM takes the overlap of all volumes after realignment, the misalignment place will be set to NaN. So if there are large head motions happened to some timepoints so that the bottom or top position of the head are out of the acquisition window (along z), SPM can't recover them back. And you will miss them after reslicing. But sometimes, the motion is less than the slice thickness, the whole or most part of the slice will still be removed. A compromise way then is to resample only after normalization (or if you can change the voxel size for resampling).
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Ze Wang, Ph.D
Assistant Professor of Biomedical Engineering,
Treatment Research Center,
Dept of Psychiatry,
Med School,
University of Pennsylvania,
3900 Chestnut St.
Philadelphia, PA 19104
Tel: 215-222-3200-123
Fax: 215-386-6770
Tel at CFN: 215-662-7341
----- Original Message -----
From: "Raimo Joensuu" <[log in to unmask]>
To: [log in to unmask]
Sent: Wednesday, October 21, 2009 11:02:41 AM GMT -05:00 US/Canada Eastern
Subject: [SPM] Slices 'lost' in beta images
Hello,
I have noticed that I lose the bottom- and topmost slices in betaimages. The matrix size is correct but the first and last slices in the 1 st level beta images are completely ‘black’, and in the 2 nd level betas 2+2 slices are black. I wonder if there is a mathematical reason for that or if there is something wrong in my setup?
Thank you in advance,
Raimo
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