Dear FreeSurfer experts,
I'm trying to implement the steps you indicate in the Paired Analysis' wiki site, but I still don't get something: In this site, you show the next FSGD file: GroupDescriptorFile 1 Class Main Variables Age Input subject1pair Main 30 Input subject2pair Main 40 Input subject3pair Main 50 Input subject4pair Main 60 Accordingly, "Age" is a variable whose value is the same for each pair of subjects (i.e., it is a measure of between-pair differences, but does not contain information about differences found in subjects of the same pair). Nevertheless, I need to introduce some covariates of interest whose value would indicate within-pair differences (i.e., the difference between "subjectN" and "subjectNmatch", where "N" is the arbitrarily assigned pair number). I made the next FSGD, but I'm wondering it's not correct (is it?):
GroupDescriptorFile 1 Title trait1_trait2_paired MeasurementName thickness Class male Class female Variables Age trait1_diff trait2_diff Input subject1pair female 24 150 1850 Input subject2pair male 41 -200 -2090 Input subject3pair female 48 50 -6508 Input subjec4tpair male 53 -100 -7100 Input subject5pair female 36 150 1950 . . .
In this FSGD, the last two variables ("trait1_diff" and "trait2_diff") would represent within-pair differences. As you can see, there are both positive and negative values, depending on the random order of individuals within a pair. Afterwards, contrast files such as "0 0 0 0 0.5 0.5 0 0" or "0 0 0 0 0 0 0.5 0.5" would be used to check whether "trait1_diff" or "trait2_diff" have an effect on cortical thickness, regressing out the effects of "gender", "Age" and either "trait2_diff" or "trait1_diff".
Could you please tell me if the FSGD table is correct? If it isn't, how to implement such an approach? (I.e., how to use both between-pair and within-pair variables?) Also, are the contrast files mentioned above correct?
Thank you in advance, Aldo