Maybe you can apply the transform using mri_convert or mri_vol2vol created during autorecon1. Is that what you are looking for?
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> _______________________________________________
On Feb 22, 2012, at 11:26 AM, Long <longspace82@gmail.com> wrote:
> Dear all,
>
> I had EPI images and T1 image and the EPI images are already co-registered to T1 image in their native space. I also run 'recon' on T1 image. I'd like to try surface-based spatial normalization in FreeSurfer, so how can I only do the spatial normalization of EPI images in FreeSurfer, i.e., transform EPI images from native space to mni152 space, then I could have surface-based normalized EPI images.
>
> Best,
> Xiangyu
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