Hi Doug, 

just following up to see if you had any suggestions for resolving the problem of the ?h.wm surfaces not pulling back even after running it through the pipeline. If you are in need of more screenshots or details, let me know. 

Thanks, 

Jacob Jensen

On Wed, Sep 30, 2020 at 8:37 AM Jake Jensen <jacobjensen673@gmail.com> wrote:

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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