Definitely #2. You should use the xhemi tools http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi First run them through recon-all as normal, then follow the steps on the wiki. Contact the list again to get instructions for the final analysis.

doug

On 02/13/2014 08:23 AM, Paola Valsasina wrote:

Dear List,

we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the images of some patients, so that the affected side is left for all subjects.

Which is the best way to do this:

1)flip the 001.mgz volume and perform the entire recon-all pipeline with flipped images;

or

2)perform the recon-all pipeline with the non-flipped volumes and flip only the final surfaces for statistical purposes?

Thank you for any suggestion

Kind regards

Paola

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