External Email - Use Caution Thanks for your patience with me. I am really appreciate. : )
Ting > On Apr 19, 2018, at 3:14 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > > The wiki and the papers :) > > > On 04/19/2018 03:22 PM, Ting Li wrote: >> 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 > > _______________________________________________ > 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
