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/FreeSurferCol... for instance left&right amygdala- + insula
and then do this: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFunct...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.josefson@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