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:
- 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