Re: [Freesurfer] Recon-all with custom atlas

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 wrote: > > The wiki and the papers :) > > > On 04/19/2018 03:22 PM, Ting Li wrote: >> External Email

Re: [Freesurfer] Recon-all with custom atlas

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

Re: [Freesurfer] Recon-all with custom atlas

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

Re: [Freesurfer] Recon-all with custom atlas

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

Re: [Freesurfer] Recon-all with custom atlas

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

Re: [Freesurfer] Recon-all with custom atlas

No, I think that is it. On 04/19/2018 02:07 PM, Khoi Mai wrote: > > External Email - Use Caution > > From what I read in the gctrain --help, does it only require > talairach_man.xfm and the manual segmentation files? Does it require > anything else for each subject? > > On Thu, Apr 19,

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution From what I read in the gctrain --help, does it only require talairach_man.xfm and the manual segmentation files? Does it require anything else for each subject? On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve wrote: > If

Re: [Freesurfer] Recon-all with custom atlas

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 > >

Re: [Freesurfer] Recon-all with custom atlas

I'm not clear on what you are trying to do. Did you apply the atlas to an individual and have the atlas ROIs in the individual brain? On 04/19/2018 12:42 PM, Ting Li wrote: > > Douglas, > > Thank you so much for your response. My atlas is nii.gz format. What should I > do to get the

Re: [Freesurfer] Recon-all with custom atlas

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

Re: [Freesurfer] Recon-all with custom atlas

External Email - Use Caution 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

Re: [Freesurfer] Recon-all with custom atlas

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

[Freesurfer] Recon-all with custom atlas

External Email - Use Caution 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