Dear Dr. Alfonso,

We have two groups of subjects: healthy (HS) and patients with schizophrenia (SZ). The SZ group can be sub-divided into patients with hallucinations (AVH+) and those who do not have hallucinations (AVH-). We ran two set of analysis (independent conn projects): the first had
HS and SZ groups (included as second level covariates). In the second project, we only included SZ subjects and had two second level covariates (AVH+ and AVH-). Both projects were analysed with the same parameters till second level.

For Project1 (HS and SZ groups):
- Selected only SZ group (in the subject effects list)
- Clicked on Results Explorer
- Selected all ROIs (and de-selected F test)

For Project2 (only SZ group; AVH+ and AVH-)
- Selected All Subjects in the subjects effects list
- Clicked on Results Explorer
- Selected all ROIs (and de-selected F test)

Upon comparing both the outputs, we found that:
- Overall connectivity pattern is almost the same (there are some minor differences)
- There is a difference in the T statistic value that we see (all values are shifted)

How do we account for the difference in the T values (as it is essentially the same set of subjects that are being analysed)? Shouldn't the values be same or are we doing something wrong somewhere?

The output from both the runs are also attached. We have ensured that in both the runs the same condition was selected (and we in fact did run the analysis a second time just to be sure).

Regards,
Pravesh Parekh