[FieldTrip] sLORETA statistics

[Bethel Osuagwu]

Deal Fieldtripers,
Since there is no forum for the software sLORETA (http://www.uzh.ch/keyinst/loreta.htm), I have decided to post here to see if I can get any help.

I am currently processing my data on sLORETA and I have noticed something regarding the statistical significance of my results. The statistical significance of activated regions of the brain depends on how I enter my data into the statistical software  of sLORETA. I put the data in the following two ways.
1)  I computed one cross spectra file with all the trials from one subject. I did this for each subject.  Then I computed sloreta file for each of the subjects' cross spectral file.
2)  I computed one cross spectra file for each trial. So I have trials*subjects number of cross spectral files. I computed the sloreta file for each trials' cross spectra file.

Now, I performed statistics comparing 1) above with its baseline and did the same with 2). I got the same activation pattern for both 1) and 2) but 2) allows more areas of the brain to be significant. To be honest two favours the areas I am interested in but I am not sure if I am deceiving the software with the method in 2). Is the software thinking that each trial in 2) is a unique subject and therefore thinks that I have trials*subjects number of subjects? Is it even a statistical issue if the software is treating my data in this way since each trial could be considered individually anyway? I just want to know why there is a difference between the statistical significance in the two methods and if there is an issue with using method 2).

Thanks for your consideration.
Bethel