Many thanks Dr. Fischl for your support. My goal is to create a mesh completed of skull and scalp to be able to perform the Monte Carlo simulation on it. To do it, I need to start from a well segmented brain, so I decided to go for FreeSurfer.
I have read something about the mri_watershed, but I could’t find any specific information about how exactly use it (my apologise, but I am quite new among the FreeSurfer users). Why do I need the T2 image to use this function? Many thanks in advance Best Chiara ---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulg...@mail.bbk.ac.uk // bulgarelli.chia...@gmail.com > On 20 Apr 2016, at 14:30, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > 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 >> cbulg...@mail.bbk.ac.uk // bulgarelli.chia...@gmail.com > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.
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