Dear Ann,
I guess with "unnormal" you refer to the fact that c1 and c2 are tilted into one direction. The c* volumes are written in the same space / voxel size as the raw data, so if your raw volume is tilted, they are going to be tilted the same way.
These misplacements are no problem, as long as they aren't too large (based on your mwc1 it seems you didn't run into troubles for this subject). The normalisation and segmentation algorithms include a step in which rigid transformations are applied to the data, which correct for these misplacements relatively to the orientation of the templates / tissue probability maps. But they aren't applied to the c1 c2 c3 volumes. If you want to check the quality of the segmentation, it's better this way (one specific voxel of your original volume corresponds to the very same voxel in the c* volumes).
Best,
Helmut
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