Hi again freesurfers, I have some beginner's problems.
I want to use some specific cortical and subcortical structures from Recon-all as ROI's in my SPM analyses. How do I extract and save these as binary masks ? Would this be a good idea: pick the structures I want from here http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT for instance left&right amygdala- + insula and then do this: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace?highlight=%28space%29|%28functional%29<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace?highlight=%28space%29%7C%28functional%29> I wonder, what is the meaning of the term "functinal space" - is it native space or in group space? And can I save individual structures, e.g. amygdala as separate masks? Best, Anna ---------- Forwarded message ---------- From: Anna Josefson <anna.b.josef...@gmail.com> Date: 2013/5/31 Subject: Conversion To: freesurfer@nmr.mgh.harvard.edu Dear FreeSurfer users! I am new to Freesurfer, and I have succesfully managed to run recon-all on my data, for every subject. Now I plan to use the output - some of the different cortical and subcortical brain structures as ROI's in my SPM analyses. Then I would have to convert from freesurfer space to SPM space via the coordinates. And - I would also have to convert from .mgz to .nii data format. Does any have any tips on how to do this? Or a script? Kind Regards, Anna B. Josefson
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