I am new to freesurfer and I am trying to understand how to best perform a cortical thickness analysis for an ROI that is not pre-defined in freesurfer, such as the IFJ or V5. Should I create a surface ROI label using tksurfer (or freeview) or should I create an ROI in volume space? What is the difference? Which way is methodologically correct? Can I obtain the average cortical thickness for my ROI if it is created as a label?  Also, is there a tutorial explaining how to draw an anatomical ROI that is not designated in either atlas, either as a label or as a volume? I would like to compare cortical thickness of my ROI to a behavioral measure in a group of subjects that were treated with TMS to this ROI. I have looked through the listserve and tutorials but I have not found my answer.

Thank you,

Elissa  
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