Hi Erik,

It goes in the same way, that is, use the seed in both runs, then combine them. The effect sizes (to be used later in a comparison across subjects) can be computed just by averaging the two runs.

For test statistics per subject, the combination is more laborious (and likely less useful). For fixed effects, you'd sum the effect sizes across the two runs, the sums of the squared residuals, the degrees of freedom, and the efficiencies, then plug these into the formula for the t-statistic. I think, though, that the above (averaging effects across runs) is probably simple and informative enough...

All the best,

Anderson

On Wed, 13 Mar 2019 at 09:08, Erik <[log in to unmask]> wrote:

Dear FSL experts
I have been unable to find a good answer for the best way of handling multiple resting-state fMRI runs in a single subject. We have acquired two rs-fMRI runs in one session and would like to combine these for purposes of a seed-based connectivity analysis. From the FSL tutorials, it seems that this is done with a fixed-effects second level analysis with task-based fMRI or ICA in FEAT, but I am unclear how you would do this with a seed-based connectivity analysis. Can this be easily done in FSL? Thanks!

Erik

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