Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seen the CSF segmentation which is inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). I'm wondering how can i have it or probably its label? Thank you!
you can't get an accurate estimate of sulcal CSF from just a T1 as you can't distinguish it from other things that are dark, so we don't geenerate a label for it
cheers Bruce On Sun, 1 Oct 2017, angel angel wrote:
Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seen the CSF segmentation which is inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). I'm wondering how can i have it or probably its label? Thank you!
I see. By the way is aseg.mgz the segmentation after surfaces ? I mean if the topology correction is considered. Thank you!
On Sunday, October 1, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
you can't get an accurate estimate of sulcal CSF from just a T1 as you can't distinguish it from other things that are dark, so we don't geenerate a label for it
cheers Bruce On Sun, 1 Oct 2017, angel angel wrote:
Dear FreeSurfer Experts,
I'm so new to the FreeSurfer. I have seen the CSF segmentation which is inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). I'm wondering how can i have it or probably its label? Thank you!
hmmm, not exactly sure what you mean, but the aseg is corrected with the topologically corrected surfaces. Note that sampling them into the volume can change the topology though
On Mon, 2 Oct 2017, angel angel wrote:
I see. By the way is aseg.mgz the segmentation after surfaces ? I mean if the topology correction is considered. Thank you!
On Sunday, October 1, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: you can't get an accurate estimate of sulcal CSF from just a T1 as you can't distinguish it from other things that are dark, so we don't geenerate a label for it
cheers Bruce On Sun, 1 Oct 2017, angel angel wrote: Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seen the CSF segmentation which is inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). I'm wondering how can i have it or probably its label? Thank you!
I mean if the holes and handles are corrected in the aseg.mgz. You mean sampling the surfaces into the volume may cause topological defects? On Sun, Oct 1, 2017 at 11:04 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, not exactly sure what you mean, but the aseg is corrected with the topologically corrected surfaces. Note that sampling them into the volume can change the topology though
On Mon, 2 Oct 2017, angel angel wrote:
I see. By the way is aseg.mgz the segmentation after surfaces ? I mean
if the topology correction is
considered. Thank you!
On Sunday, October 1, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
you can't get an accurate estimate of sulcal CSF from just a T1 asyou can't distinguish
it from other things that are dark, so we don't geenerate a labelfor it
cheers Bruce On Sun, 1 Oct 2017, angel angel wrote: Dear FreeSurfer Experts, I'm so new to the FreeSurfer. I have seenthe CSF segmentation which is
inside the ventricles in aseg.mgz but i couldn't see the peripheral CSF (the csfoutside of cortex).
I'm wondering how can i have it or probably its label? Thank you!
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yes. The surface lives in a continuum and cannot necessarily be represented on a descrete grid
On Sun, 1 Oct 2017, Fereshte wrote:
I mean if the holes and handles are corrected in the aseg.mgz. You mean sampling the surfaces into the volume may cause topological defects? On Sun, Oct 1, 2017 at 11:04 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: hmmm, not exactly sure what you mean, but the aseg is corrected with the topologically corrected surfaces. Note that sampling them into the volume can change the topology though
On Mon, 2 Oct 2017, angel angel wrote: > I see. By the way is aseg.mgz the segmentation after surfaces ? I mean if the topology correction is > considered. Thank you! > > On Sunday, October 1, 2017, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > you can't get an accurate estimate of sulcal CSF from just a T1 as you can't distinguish > it from other things that are dark, so we don't geenerate a label for it > > cheers > Bruce > On Sun, 1 Oct 2017, angel angel wrote: > > Dear FreeSurfer Experts, > I'm so new to the FreeSurfer. I have seen the CSF segmentation which is > inside the ventricles in > aseg.mgz but i couldn't see the peripheral CSF (the csf outside of cortex). > I'm wondering how can i > have it or probably its label? > Thank you! > > >_______________________________________________ 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.
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