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Hello everyone, I have problems running second level analisys. My setup is quite simple. Namely I have two groups (males and females) and each o them went through two sessions. I want to know if there is any activation present within the gender group due to a session. Therefore I guess that the two paired t test (one for males one for females) is appropriate. I prepared everthing just as it is in the online tutorial for paired t-test. However when I run the script for females in certain part of the analisys I get : ln -s ../tdof_t1.hdr tdof_filtered_func_data.hdr ln -s ../tdof_t1.img tdof_filtered_func_data.img /usr/local/fsl/bin/avwroi mask tmpmask 0 91 0 109 0 1 /usr/local/fsl/bin/avwroi filtered_func_data tmpcope 0 91 0 109 0 1 /usr/local/fsl/bin/avwroi var_filtered_func_data tmpvarcope 0 91 0 109 0 1 /usr/local/fsl/bin/flame --cope=tmpcope --vc=tmpvarcope --mask=tmpmask -- ld=stats0 --dm=design.mat --cs=design.grp --tc=design.con --ols -- nj=10000 --bi=500 --se=1 --fm --zlt=2 --zut=20 Log directory is: stats0 Setting up: No f contrasts nevs=22 ntpts=42 ngs=1 nvoxels=0 Running: nmaskvoxels=0 njumps = 10000 burnin = 500 sampleevery = 1 nsamples = 9500 and than it creates following stats directories and for males I gest something completly else: ln -s ../tdof_t1.hdr tdof_filtered_func_data.hdr ln -s ../tdof_t1.img tdof_filtered_func_data.img /usr/local/fsl/bin/flame --cope=filtered_func_data -- vc=var_filtered_func_data --mask=mask --ld=stats --dm=design.mat -- cs=design.grp --tc=design.con --ols --nj=10000 --bi=500 --se=1 --fm -- zlt=2 --zut=20 Log directory is: stats Setting up: No f contrasts nevs=20 ntpts=38 ngs=1 nvoxels=122082 Running: nmaskvoxels=8187 njumps = 10000 burnin = 500 sampleevery = 1 nsamples = 9500 so basically three lines are missing here: /usr/local/fsl/bin/avwroi mask tmpmask 0 91 0 109 0 1 /usr/local/fsl/bin/avwroi filtered_func_data tmpcope 0 91 0 109 0 1 /usr/local/fsl/bin/avwroi var_filtered_func_data tmpvarcope 0 91 0 109 0 1 and also the flame parameters are completly different. Finally both analises create reports with activations but I suspect that something wrong is going on in case of analisys for males. Can you please verify I my suspicion is right ? With best regards Michal Kuniecki