External Email - Use Caution
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
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 Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Caution
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 mailto: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 Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 Caution
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 mailto: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 Caution 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 <mailto: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 Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
Hi again, Doug,
I am just checking to make sure that the thread didn't get lost in the pile of requests, and whether or not you have had a chance to look at the surfaces I sent.
Thanks
Jake Jensen
On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen jacobjensen673@gmail.com wrote:
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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Sorry for the delay. I actually don't have any programmatic way to force this change. You can move the surface around in freeview. Under Tools->RepositionSurface. Change "Intensity" to "Coordinate", then Shift+Left click near the surface to select the point on the surface you want to move (ie, the vertex), then Shift+Ctrol+Left to click on the location you want it to move to, then hit Apply. When it is the way you like it, save the surface. Note that recon-all will not notice this change and so will over-write it if you re-run recon-all. The next version will have a way to incorporate this into recon-all.
On 10/20/2020 6:40 PM, Jake Jensen wrote:
External Email - Use Caution
Hi again, Doug,
I am just checking to make sure that the thread didn't get lost in the pile of requests, and whether or not you have had a chance to look at the surfaces I sent.
Thanks
Jake Jensen
On Tue, Oct 6, 2020 at 10:08 AM Jake Jensen <jacobjensen673@gmail.com mailto:jacobjensen673@gmail.com> wrote:
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 <mailto: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 <mailto: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 Caution 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 <mailto: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 Caution 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 <mailto: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 Caution 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Jake Jensen