Hi Rick,

Thank you very much for your helpful answers! I’ve got four more questions about the PPI demo in AFNI_data6:

1.How to do group analysis if there are many subjects ?

I ran the PPI demo[/url] following the instruction of [url=https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/AFNI_data6/FT_analysis/PPI/README.txt]README.txt and the results file PPI.full.stats.FT+tlrc was generated. See the brick labels in this dataset:

[center]http://1061.bbs.pinggu.com/forum/201704/05/023103micplzlb6rycmzy8.png[/center]

I don’t know how to do group analysis and I think there are two options for group analysis:

1) Output the Correlation coefficient (r) of the contrast (vis - aud) of each subject and then transform r to z (fisher-z transform).

```
3dcalc -a PPI.full.stats.FT+tlrc'[28]' -b PPI.full.stats.FT+tlrc'[26]' -expr 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' -prefix Contrast_R
3dcalc -a Contrast_R+tlrc -expr 'log((1+a)/(1-a))/2' -prefix Contrast_Z
```

```
And compare z values of several subjects to zero just like what we do in the classical PPI.
2)Output single-subject Correlation coefficient (r) of each condition (vis and aud seperately) and transform them.
```

```
3dcalc -a PPI.full.stats.FT+tlrc'[4]' -b PPI.full.stats.FT+tlrc'[2]' -expr 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' -prefix Vis_R
3dcalc -a Vis_R+tlrc -expr 'log((1+a)/(1-a))/2' -prefix Vis_Z
3dcalc -a PPI.full.stats.FT+tlrc'[8]' -b PPI.full.stats.FT+tlrc'[6]' -expr 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' -prefix Aud_R
3dcalc -a Aud_R+tlrc -expr 'log((1+a)/(1-a))/2' -prefix Aud_Z
```

Then compare the z values of two conditions within group using paired t-test.

Do you think which one is better? Is there something wrong with my code of outputting and transforming?

2.What’s the function of run.ppi.example.txt?

I find another file (run.ppi.example.txt[/url]) in the [url=https://afni.nimh.nih.gov/pub/dist/edu/data/CD.expanded/AFNI_data6/FT_analysis/PPI/]PPI directory. I can’t figured out what’s the function of this script. What this script want to do is an essential processing step for gPPI or not?

3.How to choose appropriate input for 3dTfitter?

The optional inputs of 3dTfitter are difference between the two PPI version:

Gang’s page:

```
3dTfitter -RHS Seed_ts.1D -FALTUNG GammaHR.1D Seed_Neur 012 0
```

PPI demo in AFNI_data6:

```
3dTfitter -RHS $pprev.seed.$TRnup.r$rind.1D -FALTUNG $hrf_file temp.1D 012 -2 -l2lasso -6
```

The options -FALTUNG and -l2lasso are so different. How to choose better inputs of these two options for my event-related fMRI?

4.The senior colleagues in our lab used almost the same gPPI codes[/url] (which is provided by Gang’s page) to fMRI data with both block and event-related design.The only modification they made to match an event-related design was to replace the Rmodel input ‘BLOCK(3,1)’ in the regression step (step6) in [url=https://afni.nimh.nih.gov/CD-CorrAna]the codes to ‘BLOCK5(1,1)’. They want to know if there are critical errors in using almost the same codes as those provided by Gang’s page to fMRI data of event-related design.

You need not to reply me until you have enough free time. I will be very appreciated!

Po