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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:
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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