[Freesurfer] Using Subcortical initial output, with fixed cortical output

Dear FreeSurfers, I am using a Linux computer with FS 5.1 Due to the known feauture in version 5.1 where Control points may adversely affect aseg but also may alter the subcortical segmentation, is it acceptable to use the initial subcortical output (before adding control points) for analysis,

Re: [Freesurfer] Using Subcortical initial output, with fixed cortical output

Hi Mark that's the way we always processed things before 5.1 and will do after 5.1, so just state what you did Bruce On Thu, 15 Nov 2012, Mark Fletcher wrote: Dear FreeSurfers, I am using a Linux computer with FS 5.1  Due to the known feauture in version 5.1 where Control points may

Re: [Freesurfer] Using Subcortical initial output, with fixed cortical output

Just wanted to mention that, in my experience at least, it isn't just that CPs in 5.1 may adversely affect the aseg, but the inclusion of CPs can actually impact the surfaces in 5.1 in places distant from the CPs themselves. So, if you are using surfaces derived from the default 5.1 recon-all,