No, I think that is it.
On 04/19/2018 02:07 PM, Khoi Mai wrote: > > 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 <mailto: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 > <mailto: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 <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
