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Thank you for the reply, That I understand. My issue is how should I set up lvl 1 feats. or the individual's feats. Should I just set the model to the empty model? ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Anderson M. Winkler <[log in to unmask]> Sent: Monday, August 14, 2017 12:29:56 AM To: [log in to unmask] Subject: Re: [FSL] comparing two resting scans Hi Jaret, Do you have 2 treatments and 2 groups (e.g., patients and controls) or just 1 group? For a single group and 2 treatments, consider this design from the manual: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#ANOVA:_2-groups.2C_2-levels_per_subject_.282-way_Mixed_Effect_ANOVA.29<https://secure-web.cisco.com/1KEVJ1AfNau7jnS_XKeeyK3C5q2UfUhJdbO98kmiyC9Y7n_CUwTx3id2bGK-NyY9dJu1EQPVlOvh3_3Bk4CErmywsXq2hAVUZS08KhIA_HtKuyeDcTGcacwXK-XIzL941dYskgWOlgBJN72j2iOwKPz2OP1wVGLRk6ALv3-g3Cu-MUFW7FLoQtjJ075hpyDhcIADM_rfdXdpvMZvigtNtiyb1jPwYscElNBnAvepxs4xYqiQ7Tk79Nrbsm3ihIe8xQF3LQMm41i493I1TlQtFlXhvROfKoDEyTWXWA135HbRQUh2J7NUNanpSIiUdxdRU1wVBuHf1wt9zVB3Q6UrPIV3iahOaWj1PtkrQChxhpug/https%3A%2F%2Ffsl.fmrib.ox.ac.uk%2Ffsl%2Ffslwiki%2FGLM%23ANOVA%3A_2-groups.2C_2-levels_per_subject_.282-way_Mixed_Effect_ANOVA.29> Here "run" is time (before or after) and "group" is the treatment received. All the best, Anderson On 12 August 2017 at 09:13, Jaret Hodges <[log in to unmask]<mailto:[log in to unmask]>> wrote: I have had some trouble setting up a comparison between resting scans that I believe is due to how I am setting up my model. I have 2 groups of participants. All participants were scanned before receiving 1 of 2 randomly selected treatments. Then they were scanned again afterwards. My biggest question is how to set up the explanatory variables. I had originally set them to empty and then tried to compare the participants in a higher level analysis but was unable. The main thing I would like to do is run a paired t-test between the two groups. But I strongly feel I am setting up the lvl 1 analyses up incorrectly.