Here are some pictures of the pial (red), wm (yellow), and orig.nofix (green) surfaces with the brainmask.mgz and wm.mgz volumes

On Wed, Sep 30, 2020 at 8:15 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Can you send pictures of the ?h.orig.nofix surface in addition to the white and pial?

On 9/29/2020 12:24 PM, Jake Jensen wrote:

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Douglas, 

 

I have attempted to edit the wm.mgz and subsequently run -autorecon2. However the ?h.white surface remains extended. 

I have attached some before and after editing pictures, which shows how the wm surface does not recede even when it is removed. 

Thanks 

On Mon, Sep 28, 2020 at 9:04 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

It looks like the orig extends too far, so try editing the wm.mgz

On 9/25/2020 11:51 AM, Jake Jensen wrote:

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Attached are a few snapshots of the ?.orig surfaces (pink), pial (red), and wm (yellow)

On Fri, Sep 25, 2020 at 7:46 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Can you show it with the ?h.orig surfaces? Those should closely follow the boundary of the wm.mgz volume

On 9/23/2020 2:11 PM, Jake Jensen wrote:

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Hello, 

I am attempting to edit a subject, but upon removing voxels where the WM and pial surfaces should not be, the WM surface does not receed (pictures are attached). 

I have attempted this with -all and -autorecon2, running it again from the original 001.mgz file, as well as attempting to run it from the beginning with -clean. The end result is consistently the same, as seen in the attached images. Additionally, it is strange that the WM surface crosses the pial. 

I could not seem to find a solution to this in the archives. 

FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: OSX mojave 

-all -autorecon2

Recon all log attached 

Thank you! 

-Jacob

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