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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:
External Email - Use CautionDouglas,
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:
External Email - Use CautionAttached 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:
External Email - Use CautionHello,
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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