Hi Andrew,

just found your mail by chance and don't see if anyone ever replied.

I would recommend to select the best scan in the cases where you have two and run everything with a single input. It is questionable if averaging 2 scans really improves anything. In gact, it may be a problem if your inputs are not balanced (e.g. if you have two groups and one of them has significantly more averaged inputs than the other), you may bias your study and pick up the differences in the inputs, rather than disease/drug.

Best, Martin

On Mon, 2012-12-10 at 17:39 +0000, O'Shea,Andrew wrote:

Hello, Our data set has two T1 weighted scans for some subjects but only one for others. Would you recommend running all subjects with no motion correction (1 scan input)? Also can files be mixed in the analysis that have had motion correction with those who have not? Thanks! -Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer