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Dear Freesurfers, sorry for the additional message but I really need your help. I'm running the retinotopy analysis to study population receptive fields on healthy subjects. Structurals have been reconstructed using "recon-all -qcache". The stimuli I used for retinotopy are: rotating wedge (45deg, counter-clockwise) for polar angle and expanding ring (out) for eccentricity. Each subject underwent retinotopy stimuli in two conditions: free normal sight and narrowed sight. So, each subject has 1 structural and 2 pairs of functionals for each condition (1 rot wedge + 1 expanding ring for each condition).
I successfully computed the 1st level analysis for each subject for each condition. Now, I'd like to check the differences in cortical activation between the two conditions to understand if we have significant effects in activations when we narrow the sight (or simply make the subtraction analysis on the 2 conditions in such a way that we can check if we really narrow the sight).
I checked on FREESURFER tutorials but I cannot find anything similar. The group analysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is for comparison between 2 different subject populations. I opted for paired analysis https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but I'm stuck with the FSGD files (I understand two FSGD files are requested) *1)*
GroupDescriptorFile 1 Class Main Input subject6ng Main Input subject6 Main Input subject7ng Main Input subject7 Main Input subject8ng Main Input subject8 Main Input subject9ng Main Input subject9 Main Input subject10ng Main Input subject10 Main Input subject11ng Main Input subject11 Main Input subject12ng Main Input subject12 Main Input subject13ng Main Input subject13 Main
*2)*
GroupDescriptorFile 1 Class Main Variables Goggles Input subject6pair Main normal Input subject7pair Main normal Input subject8pair Main normal Input subject9pair Main normal Input subject10pair Main normal Input subject11pair Main normal Input subject12pair Main normal Input subject13pair Main normal
Where the "normal" variable means in free view conditions (not narrowed). Is it well done or am I making something wrong? - I have 1 main folder for structurals, storing all subject structural folders; - 1 main folder for functionals, storing all subjects two times (normal and narrowed conditions).
Are there any other ways to compare activations on the same subjects in different conditions?
Thank you for your patience and your help, Marco