use mri_convertcheck this linkhttps://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html

Azeez Adebimpe

Date: Fri, 31 May 2013 13:23:20 +0200 From: anna.b.josefson@gmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Conversion

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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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