External Email - Use Caution Douglas,
Sorry for bother you again. Our group want to study a cohort children’s brain using Freesurfer. We prefer to register our subjects to a custom children template. The template basically is an average of all the subjects we are going to study. It is constructed by ANTs. The format is nii.gz. My questions is where I should mention this registration template in the command Recon-all? or how to get the cortical thickness, surface area and volume for various cortical regions for all subjects and perform the GLM analyses? In Freesurfer, there is a command of making own template for registration. If I generate my template from there, how can I run recon-all for the next to make sure my subjects all register to this template? and how to get the cortical thickness, surface area and volume for various cortical regions for all subjects and perform the GLM analyses? I really need your help for this. Thanks for your time. Best, Ting > On Apr 19, 2018, at 11:42 AM, Ting Li <tx...@ualr.edu> 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
