Hi all,
We've using version 5.1 to conduct a longitudinal study involving over 150 subjects with up to three time points apiece, and we're having some issues with regards to aseg in the areas around the cerebellum. Attached is an image of the problem - some dura or something else is being classified as cerebellum. It's particularly troubling because this issue is present in most of our images, but to varying degrees. We've tried adjusting the watershed parameters (using multistrip) as well as using gcut, but neither method was effective in removing the offending voxels.
It seems like our only other option is to manually edit the brainmask.mgz, but with so many subjects and time points, we're wondering if there is another automated fix that we haven't tried. Otherwise, is this something that we'll have to manually fix, or can it be left alone?
Thank you,
Michael Murray
Hi Michael,
if cerebellar gray matter is not something you are terribly interested in quantifying then you are fine.
cheers Bruce
On Wed, 20 Jul 2011, Murray, Michael wrote:
Hi all,
We've using version 5.1 to conduct a longitudinal study involving over 150 subjects with up to three time points apiece, and we're having some issues with regards to aseg in the areas around the cerebellum. Attached is an image of the problem - some dura or something else is being classified as cerebellum. It's particularly troubling because this issue is present in most of our images, but to varying degrees. We've tried adjusting the watershed parameters (using multistrip) as well as using gcut, but neither method was effective in removing the offending voxels.
It seems like our only other option is to manually edit the brainmask.mgz, but with so many subjects and time points, we're wondering if there is another automated fix that we haven't tried. Otherwise, is this something that we'll have to manually fix, or can it be left alone?
Thank you,
Michael Murray
If it is, you can try running the skullstrip step a second time.
On Jul 20, 2011, at 7:14 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Michael,
if cerebellar gray matter is not something you are terribly interested in quantifying then you are fine.
cheers Bruce
On Wed, 20 Jul 2011, Murray, Michael wrote:
Hi all,
We've using version 5.1 to conduct a longitudinal study involving over 150 subjects with up to three time points apiece, and we're having some issues with regards to aseg in the areas around the cerebellum. Attached is an image of the problem - some dura or something else is being classified as cerebellum. It's particularly troubling because this issue is present in most of our images, but to varying degrees. We've tried adjusting the watershed parameters (using multistrip) as well as using gcut, but neither method was effective in removing the offending voxels.
It seems like our only other option is to manually edit the brainmask.mgz, but with so many subjects and time points, we're wondering if there is another automated fix that we haven't tried. Otherwise, is this something that we'll have to manually fix, or can it be left alone?
Thank you,
Michael Murray
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have been working with Michael Murray on the problems we are having stripping/segmenting the cerebellum. We have tried various things, including a range of watershed parameters (1-10), gcut, as well as running these adjustments in succession (as you suggested below) with various combinations and parameter settings, but we have yet to be successful. It either does not cut much if any excess at all, or it cuts too much and takes out sections of both the cortex and the cerebellum. Are there any others ways that we may be able to address this problem, other than by adjusting watershed parameters or doing manual edits on every subject?
Thanks very much. Heather Lugar
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens Sent: Wednesday, July 20, 2011 6:38 PM To: Bruce Fischl Cc: Murray, Michael; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aseg and Cerebellum
If it is, you can try running the skullstrip step a second time.
On Jul 20, 2011, at 7:14 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Michael,
if cerebellar gray matter is not something you are terribly interested in quantifying then you are fine.
cheers Bruce
On Wed, 20 Jul 2011, Murray, Michael wrote:
Hi all,
We've using version 5.1 to conduct a longitudinal study involving over 150 subjects with up to three time points apiece, and we're having some issues with regards to aseg in the areas around the cerebellum. Attached is an image of the problem - some dura or something else is being classified as cerebellum. It's particularly troubling because this issue is present in most of our images, but to varying degrees. We've tried adjusting the watershed parameters (using multistrip) as well as using gcut, but neither method was effective in removing the offending voxels.
It seems like our only other option is to manually edit the brainmask.mgz, but with so many subjects and time points, we're wondering if there is another automated fix that we haven't tried. Otherwise, is this something that we'll have to manually fix, or can it be left alone?
Thank you,
Michael Murray
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Allison Stevens -
Bruce Fischl -
Lugar, Heather -
Murray, Michael