Hi Elissa

I would create the ROI on the fsaverage surface using either freeview or tksurfer. You can then use mri_label2label to map it to any subject, and mris_anatomical_stats -l <label name> ... to compute thickness within the ROI cheers Bruce

On Mon, 23 Nov 2015, Elissa Ash wrote:

Dear list,

I am resending a message that I sent on Friday. Any help would be most sincerely appreciated.

Dear Freesurfers, 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   -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center

6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

-- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center

6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365