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Good afternoon,
I have some questions about the analysis of the structural data in Freesurfer, it's the first I use this programm and I'm a bit lost. In order to do the recon-all command, where should I put the T1 weighted images of my subjects (3 different groups with a total of 63 subjects)? Should I put them in the subjects folder of the freesurfer folder (i.e. SUBJECTS_DIR) or should I create a new folder in this subjects folder or should I put them elsewhere? And then should I change the working directory on the terminal so the program can find my subjects? And for the recon-all command itself, once the T1 images are found, should I just write recon-all in the terminal and the preprocessing will start?
Thanks a lot in advance for your answer! I really appreciate your help!
Have a nice day.
Best regards, Yéléna Le Prieult