Dear freesurfer experts, I have a question regarding how to incorporating bbregister coregistered mean image into the SPM batch.
After realignment step, I convert the mean functional image from the analyze format to nii format (to avoid flipping brain using bbregister)
Then, I use bbregister to co-register the mean functional image to subjects' surfaces using following command
bbregister -- s subject_name_freesurfer -- mov mean.nii --init-spm -- bold --reg register.dat -- spm-nii
After this step, is the mean.nii the coregistered image already? If it is, in SPM, shall I skip the coregistration and segmentation step? If I do skip them, in the Normalization step, is the following correct?
source image: mean.nii that has been coregistered in bbregister
image to write: (Dependency) realigned session1 and realigned session2
template image: EPI
Thank you very much for your help.
Helen