Hi John,
The reason your images are misaligned after coregistration is that you got the source and reference images the wrong way around: you move the SPGR source to fit the mean EPI reference, and the apply the transformation to the other EPIs. This mean that
a) the structural and EPIs will still be in the same relative positions: if they began unaligned, they will stay unaligned
b) the EPIs will no longer be in register with the mean EPI
I think you wanted to move the mean EPI source to fit the SPGR reference, and then move the other EPIs along with it. However, as others have already said a more straightforward approach would be to coregister the SPGR with the mean EPI (leaving the other EPIs alone). You can subsequently use your normalisation parameters on both sets of images.
This approach holds also using Marko's additional initial coregistration of the structural to the T1 template, which is intended to improve segmentation. This would go in between the SPGR-EPI coregistration and normalisation:
1) Realignment
2) Coregister SPGR source to EPI reference
3) [Optional] Coregister SPGR source to T1 template reference, taking along EPIs as other images
4) Normalisation / segmentation
5) Write normalisation parameters for SPGR and EPIs.
Hope this helps,
Paul
|