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
