External Email - Use Caution From what I read in the gctrain --help, does it only require talairach_man.xfm and the manual segmentation files? Does it require anything else for each subject?
On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > 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 >
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