Dear Marina,
the Dartel deformations u_rp1* describe the transformations from the rigidly aligned images to your customized template. However, your fMRI data were probably co-registered to the native T1-images, but not to the rigidly aligned T1 images. Try to co-register the fMRI to the corresponding rp1*affine.nii T1 image which should solve this issue.
Best,
Christian
On Mon, 11 Feb 2019 18:02:38 +0000, Marina Papoutsi <[log in to unmask]> wrote:
>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).
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>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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