Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there a more specific goal?
hth d On 10/19/15 10:56 AM, Hutton, Seth wrote: > Dear users, > > I have been using FreeSurfer for a while now, but am working in a new > lab and their goals fall outside of my realm of experience. > We are using both MRI imaging as well as FNIRs. We have multiple vitamin > E capsules placed during both and would like to be able to view them in > FreeSurfer so that we can better estimate the projected cortical > localization of these capsules. > Using the generic recon-all -s -i -all we are unable to see our > capsules, as they are most likely eliminated during the skull strip > step. I see that I can change the threshold with "-wsmore", but am > wondering if this is really the best way to accomplish what we are > trying to do. > Is there any way to include our capsules without excluding the skull > strip? If not could how would you recommend adjusting the threshold. > I tried excluding the skulls trip step with > recon-all -s -i -autorecon1 -noskullstrip > but then when I tried to view it using free view it was unable to open > due to the lack of the brain mask.mgz. > > Thank you so much for your time and consideration, > Seth H > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not > be used for urgent or sensitive issues > > > > _______________________________________________ > 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
