Hello pt, thank you again for these questions and sharing your insights!

(C1) So, if you use 3dNetCorr to calculate a wholebrain correlation map, that is done by averaging the time series within each ROI and calculating each map. That is fine—is that what you want?

Yes, I think this would be in corresponding to what I did in CONN I believe.

(C2) And did you make the perform an analogous calculation in Conn, or did you put the output from C1 into the Conn clustering, as well?

I did not put the output from C1 into the conn clustering, but to my best knowledge, I made an analogous calculation in CONN.

(C3) If you did calculate the wholebrain correlation map separately in Conn, were those pre-threshold results the exact same?

I did not check this previously, but I will.

(B1) Is that threshold the p-value threshold for voxelwise thresholding? If so, that isn’t very small… I would expect larger differences between software for larger p-values.

Sorry, I didn’t made it clear in my last message. So I used p<0.001 for voxelwise thresholding for each analysis, and p<0.01 for cluster-wise threshold.

(B2) & (B3) I will double check!

(B4) What is your exact 3dClustSim command? Are you using the mixed ACF model, described here.

Yes, the code that I use is:

```
3dClustSim -acf 0.567915926 5.510608025 14.86245309 -mask GM_msk333_final+tlrc.
```

“0.567915926 5.510608025 14.86245309” these numbers were the averaged value of the output from the preprocessing of all scans: “blur estimates (ACF)”

Did I use this correctly?

Thank you again!

Jiaxu