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

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