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Dear experts, I'm performing a study on visual pathways, in which each participant undergoes to 2 different conditions. One in normal sight (NG, i.e.: No Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes Goggles). I'd like to compare the results between these two conditions (basically, subject A, B, C in cond1 versus subject A, B, C in cond2).
I created the FSGD file (attached as "RetinotopyStudy" file) and the contrast matrices, organised as:
1 -1 , named "YG-NG.mtx"
-1 1, named "NG-YG.mtx"
In this FSGD sample file, I reported only subjects from 7 to 12. My folders are organised as follows:
main >> recon_output >> sub-yy (X folders for X subjects)
>> Contrasts (with contrast files) >> FSGD (with FSGD files) >> fsaverage (subjects templatecreated during recon-all -qcache) >> pRF_function >> analNG (inside, there are the functionals for each subject in NG condition) >> analYG (inside, there are the functionals for each subject in YG condition)
Once I used the pipeline for the retinotopy analysis http://freesurfer.net/fswiki/FsFastIndividualRetinotopyAnalysisand I have results for each participant, and now I'd like to make 2nd lev analysis. So the idea would be, as you probably already got it, condition Yes Goggles versus condition No Goggles. I use the command:
mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out
outputname.mgh
But I'm not sure it would calculate in the right way. The question is: how would I organise the FSGD file or folders in such a way that FREESURFER would know that it has to compare results from the same subjects but from two different folders (analNG vs analYG)?
Hoping that's clear, I really look forward to hear from you soon. Thank you for your time, Marco