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I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used?
Aaron Tanenbaum
External Email - Use Caution
So I never got a response for my question. At least can someone tell me the recon-all flags needed after editing the aseg.presurf.mgz file. I am also assuming that this feature is also available for 7.1.1.
On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum < aaron.b.tanenbaum@gmail.com> wrote:
I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used?
Aaron Tanenbaum
I don't have any example, but the idea is pretty simple. If you want to freeze a point on the surface, open aseg.presurf.mgz and the surfaces for your subject, eg, tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs Then edit the aseg.presurf.mgz to change the voxels where you want to freeze to value 247 (FreezeSurface in $FREESURFER_HOME/FreeSurferColorLUT.txt) Then run recon-all with -autorecon2-surfonly -autorecon3
On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
So I never got a response for my question. At least can someone tell me the recon-all flags needed after editing the aseg.presurf.mgz file. I am also assuming that this feature is also available for 7.1.1.
On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote: I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used?
Aaron Tanenbaum
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you for responding. So before you responded, I tried a few things out. one of them was to make the edit to the image and then run recon-all with "-autorecon2-noaseg -autorecon3". I found this to move the surface however the aparc+aseg file had the voxel I altered as 247. Last night I tried what you suggest with the same alterations to the aseg.presurf file, I found the surface and aparc+aseg was unchanged.
On Wed, Dec 23, 2020 at 12:28 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
I don't have any example, but the idea is pretty simple. If you want to freeze a point on the surface, open aseg.presurf.mgz and the surfaces for your subject, eg, tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs Then edit the aseg.presurf.mgz to change the voxels where you want to freeze to value 247 (FreezeSurface in $FREESURFER_HOME/FreeSurferColorLUT.txt) Then run recon-all with -autorecon2-surfonly -autorecon3
On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:
External Email - Use CautionSo I never got a response for my question. At least can someone tell me the recon-all flags needed after editing the aseg.presurf.mgz file. I am also assuming that this feature is also available for 7.1.1.
On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum < aaron.b.tanenbaum@gmail.com> wrote:
I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used?
Aaron Tanenbaum
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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so, does that mean it is working?
On 12/24/2020 12:19 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Thank you for responding. So before you responded, I tried a few things out. one of them was to make the edit to the image and then run recon-all with "-autorecon2-noaseg -autorecon3". I found this to move the surface however the aparc+aseg file had the voxel I altered as 247. Last night I tried what you suggest with the same alterations to the aseg.presurf file, I found the surface and aparc+aseg was unchanged.
On Wed, Dec 23, 2020 at 12:28 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: I don't have any example, but the idea is pretty simple. If you want to freeze a point on the surface, open aseg.presurf.mgz and the surfaces for your subject, eg, tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs Then edit the aseg.presurf.mgz to change the voxels where you want to freeze to value 247 (FreezeSurface in $FREESURFER_HOME/FreeSurferColorLUT.txt) Then run recon-all with -autorecon2-surfonly -autorecon3
On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
So I never got a response for my question. At least can someone tell me the recon-all flags needed after editing the aseg.presurf.mgz file. I am also assuming that this feature is also available for 7.1.1.
On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum <aaron.b.tanenbaum@gmail.commailto:aaron.b.tanenbaum@gmail.com> wrote: I am curious about a feature introduced in FS 7.0 In the release notes it says, "Ability to freeze the surface at points labeled 247 in the aseg.presurf.mgz" I was interested to know what this feature can do. Do you have any examples of when this should be used?
Aaron Tanenbaum
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Greve, Douglas N.,Ph.D.