I'm not clear on what you are trying to do. Did you apply the atlas to an individual and have the atlas ROIs in the individual brain?
On 04/19/2018 12:42 PM, Ting Li wrote: > > Douglas, > > Thank you so much for your response. My atlas is nii.gz format. What should I > do to get the cortical thickness, surface area and volume for various > cortical regions? Thanks in advance. > > Best, > Ting > > >> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> >> wrote: >> >> Is the atlas in GCA format? If so, then you can use gca-apply >> >> >> On 04/19/2018 10:09 AM, Ting Li wrote: >>> Hi Freesurfer Experts, >>> >>> We want to run recon-all with a custom atlas which is generated from >>> ANTs multivariate template construction. What is the right procedure >>> to run recon-all? Run recon-all to my atlas itself first and them use >>> this output as a template or I use the custom template directly. I >>> looked up your email database to search related topic and got lost. I >>> have sent another email to your group and no response received. Please >>> help me. >>> >>> Thanks for you time. I look forward to hearing from you. >>> >>> Best, >>> Ting >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
