External Email - Use Caution Douglas,
I have one more question. Do I need an accurate surface template for my surface-based analysis? Does this ( https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates <https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates> ) is the right way to go? Thanks for your time. Best, Ting > On Apr 19, 2018, at 2:22 PM, Ting Li <tx...@ualr.edu> wrote: > > 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 >
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