Dear Freesurfer experts,

                                   I have a general question regarding data 
analysis. Our group has collected data from patients with OA, some of them 
received treatment on their left leg, some of them on their right leg. We would 
like to flip the brain for the people that received treatment on their left leg 
to match the right leg group. Next, we would like perform group analysis on 
them. My question is, when should we flip the brain for the left leg group 
patients? Should we flip the raw images before we do any preprocessing at the 
individual level? Or should we flip the first level contrast images when we get 
some results for each of these subjects? I tried to flip the contrast images, 
but it seems to give me a lot of error at the second level group analysis 
level. It says that the flipped contrast image does not match the unflipped 
contrast image in orientation. Thank you very much.


Helen
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