If you want to do a surface-based analysis, then you don't need to have an accurate volume template. If you want to use a custom volume-based segmentation atlas, then you'll need to run gcatrain and gca-apply
On 04/19/2018 01:28 PM, Ting Li wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
