Thank you Gang for your prompt response and your help, I really appreciate it.
- I have 4 missing data for Run1, 2 for Run2, and 4 for Run3. Do you think I just should forget about using 3 runs with 3dlme and only use Run2 and simple 3dttest++ for the group analysis?
- Difference between runs is not the null hypothesis. The runs are similar and I do not expect any difference between them. The reason I collected 3 runs was that I could expect having several missing runs due to the nature of my study and wanted to make sure at least I have one usable run from each subject. I hope I could make it more clear.
- It is a little bit confusing for me to assign the model and ranEff. Assigning ranEff '~1' means each subject has its own intercept (please correct me if I am wrong) which is the case for my study, but not sure what -model "Time" means? Basically, I want to test the mean across input subjects datasets against 0, i.e. f I wanted to use 3dttest++ I would use the following script:
3dttest++ -overwrite -prefix t_test_T1_${name_output[$out_count_name]} -setA \
S1/T1/GLM/stats.S1_REML+tlrc'['$brk']' \
S2/T1/GLM/stats.S2_REML+tlrc'['$brk']' \
S3/T1/GLM/stats.S3_REML+tlrc'['$brk']'
.
.
.

Thanks again for your help and your time.

Best Regards,
Ahmad