Hello all,
Apologies if this is explained elsewhere, but I have gone through the archives and also scoured the FSL wiki to no end and can't seem to find a straight answer.
I am in the midst of analyzing a simple paired t-test design using fMRI BOLD data. I have 9 subjects with 2 session each, with each session containing 2 runs. This is a within-subject design with each subject getting Condition A in one session and Condition B in the other session (I would be interested in looking at the Condition A - Condition B differences at a group level). I have run my first level analysis on each run, and now I have come to run the point of setting up my paired t test design.
The FSL wiki examples only demonstrate cases with seemingly 1 run per "measure" (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#Single-Group_Paired_Difference_.28Paired_T-Test.29).
My question is, what do you do if you have more than one run per session? Can you run a first 2nd-level analysis to combine runs (in my case combining runs 1 and 2 to create a .gfeat directory) and then use the resulting cope.feat images in the 3rd level paired analysis (then running the analysis for the # of copes you have in your design)?
OR, should you combine your runs at the nifti level (using fslmerge?) and then run those through a first level analysis to input into your paired design (or use fslmaths to compute the difference between the two merged runs in Condition A and Condition B)?
Are both acceptable?
Thanks so much.
Best,
Gabriella
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