Hi Chiara
you can look at the mri_watershed help to see how to generate other tissue classes or boundary models, but typically you need some other image contrast(s) like T2/PD. What are you trying to accomplish?
As for your second question, you should be able to use mri_surf2surf with the talairach.xfm to convert the surfaces to MNI coords, or just map to fsaverage which I believe is already in MNI space.
cheers
Bruce
On Wed, 20 Apr 2016, Chiara Bulgarelli wrote:
Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am
trying to segment some structural images of infants data.
After the classical segmentation done with the ‘-recon all’ function, I am
stuck with two issues:
1. How can I add the CSF, the skull and the scalp in my model? I know that
with FS you can get just WM and GM.
2. How can I convert the RAS coordinates to MNI ones?
I have been trying to look at these topics on line and on the FreeSurfer
website, but I haven’t find anything useful so far.
Many thanks in advance for your help!
Best Regards
Chiara
----------------
Chiara Bulgarelli
PhD Student, Centre for Brain and Cognitive Development
Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
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