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Be aware that the two scans may actually have different diffusions vectors applied to them (if these were specified XYZ and if you angualted the slices). Cheers- Andreas -----Ursprüngliche Nachricht----- Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Matt Glasser Gesendet: Sonntag, 20. Januar 2008 20:43 An: [log in to unmask] Betreff: Re: [FSL] DTI-- mean of two runs The mean will have better SNR than the individual scans. You could do something like this to motion correct your data and get the mean: fslmerge -t big4d <data1> <data2> eddy_correct big4d big4d_corr 0 fslroi big4d_corr av1_corr 0 <# of volumes in a single average> fslroi big4d_corr av2_corr <# of volumes in a single average> <# of volumes in a single average> fslmaths av1_corr -add av2_corr -div 2 <data> These commands merge the two averages into a single file for motion correction, then split out the motion corrected averages, and then get the mean. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Jiansong Xu Sent: Sunday, January 20, 2008 2:31 PM To: [log in to unmask] Subject: [FSL] DTI-- mean of two runs Dear Friends: I'm using FSL (FDT) to analyze DTI data acquired with a Simens Trio 3 T scanner. Each subject had two scans with same parameters. My question is: is the mean image of the two scans better than either one of the two scans? If so, how to get the mean of the two images? Best Jiansong