You can use mkheadsurf to create a surface of the outside of the head On 04/20/2016 10:59 AM, dgw wrote: > Hi Chiara, > > look at the -surf option and the -useSRAS option > > > We often use multi-echo FLASH/ PD images for generating these > surfaces, because standard MPRAGE type sequences lack contrast for > bone, see figure 17 here: > http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed.pdf > > hth > d > > On Wed, Apr 20, 2016 at 10:44 AM, Chiara Bulgarelli > <cbulg...@mail.bbk.ac.uk> wrote: >> 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. >> >> >> >> _______________________________________________ >> 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. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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