Hi Helen, I would follow these steps http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi this describes the interhemispheric analysis assuming that you want to study asymmetry. This is not quite your application, but I think it will work well for it. In general, you don't want to simply left-right reverse the pixel data because the atlases used in processing implicitly incorporate any left-right asymmetry that existed in the training data. doug

On 11/20/2012 12:36 PM, Chen, Xiaoyan wrote:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer