Dear All,
I am stuck. Several brains I segment need both wm and pial edits, typically deleting incorrectly incorporated voxels, such as dural voxels for pia, and basal temporal hyperintensity artifact or bright dural voxels included due to partial volume effects for wm.
I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz for wm. Rerunning recon-all led as expected to pial correction, however wm edits did not end up in ?h.white, despite increasingly desperate efforts and commands:
recon-all -autorecon2-wm -autorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all
Please advise, I could FTP one subject to you for suggestions. Again, edits here are all voxel deletions and not additions to wm.mgz. Thank you, Octavian
Hi Octavian
what tool are you using for the deletion of wm voxels? Make sure it is the "recon editing" tool in freeview or the equivalent. We do NOT set voxels to 0 when you erase - we set them to 1. This allows us to detect the erasure and preserve it during reprocessing.
cheers Bruce
On Fri, 31 Mar 2017, Octavian Lie wrote:
Dear All,
I am stuck. Several brains I segment need both wm and pial edits, typically deleting incorrectly incorporated voxels, such as dural voxels for pia, and basal temporal hyperintensity artifact or bright dural voxels included due to partial volume effects for wm.
I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz for wm. Rerunning recon-all led as expected to pial correction, however wm edits did not end up in ?h.white, despite increasingly desperate efforts and commands:
recon-all -autorecon2-wm -autorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all
Please advise, I could FTP one subject to you for suggestions. Again, edits here are all voxel deletions and not additions to wm.mgz. Thank you, Octavian
Dear Bruce,
I am using the recon editing and all voxels removed are 1. If this is the correct value for removed wm voxels during editing, Is there a way I could send you a subject? Thank you,
Octavian
On Sat, Apr 1, 2017 at 8:47 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Octavian
what tool are you using for the deletion of wm voxels? Make sure it is the "recon editing" tool in freeview or the equivalent. We do NOT set voxels to 0 when you erase - we set them to 1. This allows us to detect the erasure and preserve it during reprocessing.
cheers Bruce
On Fri, 31 Mar 2017, Octavian Lie wrote:
Dear All,
I am stuck. Several brains I segment need both wm and pial edits, typically deleting incorrectly incorporated voxels, such as dural voxels for pia, and basal temporal hyperintensity artifact or bright dural voxels included due to partial volume effects for wm.
I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz for wm. Rerunning recon-all led as expected to pial correction, however wm edits did not end up in ?h.white, despite increasingly desperate efforts and commands:
recon-all -autorecon2-wm -autorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all
Please advise, I could FTP one subject to you for suggestions. Again, edits here are all voxel deletions and not additions to wm.mgz. Thank you, Octavian
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sure, upload one and give us detailed instructions on how to find what you think the problem is (like voxel coords of where you made an edit that didn't result in the modifications you thought it would)
cheers Bruce
On Sat, 1 Apr 2017, Octavian Lie wrote:
Dear Bruce,
I am using the recon editing and all voxels removed are 1. If this is the correct value for removed wm voxels during editing, Is there a way I could send you a subject? Thank you,
Octavian
On Sat, Apr 1, 2017 at 8:47 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Octavian
what tool are you using for the deletion of wm voxels? Make sure it is the "recon editing" tool in freeview or the equivalent. We do NOT set voxels to 0 when you erase - we set them to 1. This allows us to detect the erasure and preserve it during reprocessing. cheers Bruce On Fri, 31 Mar 2017, Octavian Lie wrote: Dear All, I am stuck. Several brains I segment need both wm and pial edits, typically deleting incorrectly incorporated voxels, such as dural voxels for pia, and basal temporal hyperintensity artifact or bright dural voxels included due to partial volume effects for wm. I edited brainmask.mgz or brain.finalsurfs.manedit.mgz for pia, and wm.mgz for wm. Rerunning recon-all led as expected to pial correction, however wm edits did not end up in ?h.white, despite increasingly desperate efforts and commands: recon-all -autorecon2-wm -autorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all Please advise, I could FTP one subject to you for suggestions. Again, edits here are all voxel deletions and not additions to wm.mgz. Thank you, Octavian
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Octavian Lie