I edited the wm.mgz according to the guide, but it didn't change anything when I ran the reconstruction.
What is the brush value supposed to be when editing? 255?
On Tue, 2017-02-28 at 08:33 -0500, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Manual edit to include missing cortex? (Rockers, Elijah D.)
- Re: Manual edit to include missing cortex? (Lee Tirrell)
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Message: 1 Date: Mon, 27 Feb 2017 21:45:39 +0000 From: "Rockers, Elijah D." edrockers@houstonmethodist.org Subject: [Freesurfer] Manual edit to include missing cortex? To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 1488231939.3484.60.camel@houstonmethodist.org Content-Type: text/plain; charset="utf-8"
Is there something I can do to extend the pial surface to include cortex that it ignored? In some places there are rather large chunks of cortex not included in the pial surface.
https://urldefense.proofpoint.com/v2/url?u=http-3A__imgur.com_a_FnAgj&d=...
Link is to a screenshot, notice the top of the brain. It's fairly pronounced, visible in 12 adjacent sagittal slices.
I tried using the "Reposition Surface" tool, but I'm not exactly how it works, and I ended up just making the surface look crazy there.
I also tried adding control points in the white matter near the edges of the WM surface by the problem and ran the reconstruction, as someone in the archives suggested, but it didn't change the surface.
Thanks for your help, Eli
Houston Methodist. Leading Medicine.
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Message: 2 Date: Mon, 27 Feb 2017 17:51:06 -0500 (EST) From: Lee Tirrell ltirrell@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Manual edit to include missing cortex? To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.17022717... > Content-Type: text/plain; charset="iso-8859-7"
Dear Eli,
You may have to draw in voxels in the wm.mgz volume if it doesn't extend out far enough. After rerunning, this will push out the white surface, which causes the pial surface to be positioned further out. You can refer to our tutorial page for more information: https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
Specifically, the "Edits to the wm volume (segmentation error)" section explains the types of changes you may have to make: https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
After making the changes, re-run with this command: recon-all -autorecon2-wm -autorecon3 -s subject_name
Let me know if you have further questions.
Best, Lee
On Mon, 27 Feb 2017, Rockers, Elijah D. wrote:
Is there something I can do to extend the pial surface to include cortex that it ignored? In some places there are rather large chunks of cortex not included in the pial surface.
https://urldefense.proofpoint.com/v2/url?u=http-3A__imgur.com_a_FnAgj&d=...
Link is to a screenshot, notice the top of the brain. It's fairly pronounced, visible in 12 adjacent sagittal slices.
I tried using the "Reposition Surface" tool, but I'm not exactly how it works, and I ended up just making the surface look crazy there.
I also tried adding control points in the white matter near the edges of the WM surface by the problem and ran the reconstruction, as someone in the archives suggested, but it didn't change the surface.
Thanks for your help, Eli
Houston Methodist. Leading Medicine.
U.S. News & World Report has recognized Houston Methodist as one of the nation?s top 20 hospitals, placing it for the second time on the magazine?s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHos... and https://urldefense.proofpoint.com/v2/url?u=http-3A__www.facebook.com_Houston... .
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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