Dear Michael,
thanks a lot for your response! I tried to put the dof option on the first line and deleted it from the second, like:
flirt -in SUBJ_ANAT_IMAGE -ref $SUBJ_CENTRAL_FUNC_IMAGE -out S2F_Filename -dof 6
flirt -in S2F_Filename -ref MNI_2mm_Template -out S2F2T_Filename -omat str2func2templ.mat
but in this case the second coregistration goes all distorted (see attachment) and as a consequence also the functional to template. Can you help? Thanks!
best
Elena
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