Hi Anna, if you just want to create a binary mask, you can use
mri_binarize --i aparc+aseg.mgz --match 18 54 1035 2035 --o amyg+insula.nii
this will give you a binary mask of amygala and insula
doug
On 6/12/13 10:50 AM, Anna Josefson wrote:
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
<mailto:anna.b.josef...@gmail.com>>
Date: 2013/5/31
Subject: Conversion
To: freesurfer@nmr.mgh.harvard.edu <mailto: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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