Dear all,
I am having a problem coregistering my functional data to MNI template. I am executing the following sequence of FLIRT commands:
#Structural to functional space
flirt -in SUBJ_ANAT_IMAGE -ref $SUBJ_CENTRAL_FUNC_IMAGE -out S2F_Filename
#(Structural to Functional) to Template space (dof=6 for same subject)
flirt -in S2F_Filename -ref MNI_2mm_Template -out S2F2T_Filename -omat str2func2templ.mat -dof 6
#Functional to Template Space using parameters from the previous transformation
flirt -in FuncData_Run -ref MNI_2mm_Template -out F2T_filename -init str2func2templ.mat -applyxfm
However, when viewed with the template overlaid, the subject's brain is visibly smaller. Anyone can tell me what went wrong? Thanks a lot and have a nice weekend.
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