On Apr 19, 2018, at 2:22 PM, Ting Li <txli1@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 <dgreve@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 <txli1@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 <dgreve@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


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