Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
Hello Bruce,
thank you very much for your fast response and clarifying that potential voxels outside the pial surface do not impact cortical measures.
Best, Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question.
In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools.
Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate?
Thus, voxels, which have not been automatically labelled would not impact volume computations?
Thank you kindly for your help.
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exactly, or measures derived them them like whole-brain volume
cheers Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Hello Bruce, thank you very much for your fast response and clarifying that potential voxels outside the pial surface do not impact cortical measures.
Best, Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces. cheers Bruce On Sun, 5 Jan 2014, Yuliya Yoncheva wrote: Dear FreeSurfer community, I am visually inspecting the quality of my recon -all output for a large dataset and have a rookie question. In some instances, when skull stripping ended up leaving some of the skull, these voxels are associated with a "sgmtn label" (cerebral cortex). In other instances, although there are a small number of skull voxels that were not removed automatically, these voxels do not have an associated "sgmnt label" available in TkMedit Tools. Is it the case that only the voxels for which there is a segmentation label are actually added to the total grey volume estimate? Thus, voxels, which have not been automatically labelled would not impact volume computations? Thank you kindly for your help.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 -
Yuliya Yoncheva