External Email - Use Caution Douglas,
Thanks for your quick response. If I only want the information of cortical thickness, surface area, volume for various cortical regions and LGI, then the Freesurfer template is good enough and I don’t need to apply my own template. This is really helpful. Is there any documents that you will recommend to get a better understanding about Freesurfer? Thanks a lot. Ting > On 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
