That is, but since that wiki was written, I've written a script called make_folding_atlas. It takes quite a while to run through the 10 or so iterations. You might not need it as surface-based registration is much less sensitive to brain changes than volume-based.
On 04/19/2018 04:05 PM, Ting Li wrote: > > > 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 ) 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 >> <mailto: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 <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 >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> 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 >> > > > > _______________________________________________ > 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
