Hi,
I used CAT12 to segment my structural images. Because my data come from a patient population with atrophy, I used Dartel to create a template using the rp1* images. The template looks very good.
For VBM, I normalized the rp1*affine.nii images using the u_rp1*Template. nii deformation fields.
The resulting smwrp1* images look good and are all in the same space across participants.
I then wanted to apply the same normalization to the fMRI images. For this purpose, I used the same deformation image as above (u_rp1*Template.nii) and applied to my EPI images.
I applied the same process to create a mean structural image across my group for visualisation purposes, but noticed that the normalized structural images are not well-aligned. The attached image shows the normalized images from two participants. The contours show how the top participant overlaps to the bottom one).
I have checked the EPI images and it does seem that the same happened to them, although it is harder to spot because of the low resolution.
I also double checked and the p1* images are completely aligned to the non-normalized structural images.
Can you advise on what is going on and how to fix this?
Many thanks,
Marina
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