Hi,

thank you for your quick answer.

>> Concerning Fisher transforms. AFNI proposed that we do it before running seed-based analysis.
> No, that's not true. Fisher transformation is typically performed after the seed-based correlation analysis at the individual level, but before group analysis. Such practice is typically adopted in the whole neuroimaging community.

Yes, sorry, I wrote too fast, that is indeed what we are doing.

>> I have come upon some situations where I think it creates false results. Under the seed, the correlation
>> coefficients should be really high, because the seed should be well connected with itself. Let's say ~1.
>> However, after the Fisher correction, in my case, it becomes 1.6 in one group, and 1.1 in another, and it
>> results in significant difference in the seed region between the two groups. Obviously, I can't state that
>> connection of the seed with itself is different in both groups!
> Without knowing your analysis steps and without access to your data, it's hard to tell why and how you got what you're seeing.

We are doing a typical uber_subject preprocessing, on two groups (patient subjects vs healthy controls), on resting state data, 5 minutes.
The only thing that could be tricky is that the healthy subjects come from a different data bank (different scanner, not exactly the same TR). We are only exploring the feasibility of such a study. So far, the results follow the literature, so I would think that it won't be a problem.
I did the seed-based with 3dfim+ with 5mm seeds (voxels are 3.5x3.5x3.5mm), then fisher transform, and then 3dttest++ on the two groups.


>> Then how do I know that Fisher transforming the data is a good idea?
> Fisher transformation is not something opaque: [en.wikipedia.org]

Yes, thank you, I will read it carefully. But I am not worried about the mathematical side of the fisher formula, but rather it's effect on seed-based analysis on fMRI data.


Should I just ignore results that are close to the seed position? Is it something that happens a lot?