Re: [Freesurfer] WM edit, remove GM bright rim

Hi Min unfortunately there's not much we can do as these artifacts make the gray matter look just like white matter. Do you see this in many subjects? sorry Bruce On Thu, 17 Mar 2016, Min Liu wrote: Dear Bruce,  Many thanks for looking into this. I tried to post orig.mgz to the mailing

[Freesurfer] WM edit, remove GM bright rim

Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some spots like the one showing in the attached Figure 1. The WM surface goes out to include this bright signal and the cortex ends up artificially thin. We followed the standard WM edit procedure, which is

Re: [Freesurfer] WM edit, remove GM bright rim

Hi Min that looks like it might be a normalization problem. Can you post the orig.mgz and see what it looks like? Is there a bright rim in it also? cheers Bruce On Wed, 16 Mar 2016, Min Liu wrote: Dear Freesufer users, We have some T1 images having a rim of bright signal in the GM at some

Re: [Freesurfer] WM edit, remove GM bright rim

Dear Bruce, Many thanks for looking into this. I tried to post orig.mgz to the mailing list yesterday but the email didn't get through because the file size exceeds 1000KB. So I screen-captured two images to showcase the overall quality of T1 and where the problem is. Although the bright rim

Re: [Freesurfer] WM edit, remove GM bright rim

Dear Bruce, Thank you very much for your reply. I think we will discard these subjects for the analyses. Thanks, Min On Thu, Mar 17, 2016 at 9:53 AM, Bruce Fischl wrote: > Hi Min > > unfortunately there's not much we can do as these artifacts make the gray > matter