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Are you referring to -T and -n (rather than -t)? If you actually are using -t, what target image are you specifying? Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Deryk Beal Sent: Tuesday, September 23, 2008 3:31 PM To: [log in to unmask] Subject: [FSL] tbss_2_reg -t & -n differing results (repost) Hello FSL users My apologies for the repost but I did not receive a response and I am hopeful I will this time around. Thanks:) Deryk I have processed my data using tbss_2_reg -t & -n options. All things being equal the statistics come out dramatically different. I have a control (n=14) and patient group (n=15) and both are men aged 20-49. My questions are: 1. Is it typical to expect large differences in the statistical results (e.g., increased and decreased FA in very different locations) when the -t vs. -n options are used especially in men (who I would predict would match well to the MNI template)? 2. Seeing as the results are so different which set of data do I trust? I am assuming in this case that I would trust the data generated with the -n option as this should be most representative of my sample. 3. As a side, is it appropriate to trust the atlas labels in the atlas toolbox if your sample has not been normalized to that atlas (e.g., JHU labels when the default MNI template was used as the target)? Cheers, Deryk