I am trying to use FreeSurfer to measure ventricular volume among patients with normal pressure hydrocephalus. I have run the first subject, whose ventricles are huge. When looking at the subcortical segmentation (aseg.mgz) in tkmedit, I saw that large portions of the ventricles are labeled as cerebral white matter or white matter hypointensities. I tried filling in the ventricles in the wm.mgz volume and then running autorecon2-wm, but this does not appear to have changed anything in the aseg.mgz segmentation nor in the aseg.stats file. Is there a way I can correct this problem, and/or prevent it when I run more NPH patients?
Thanks, Dana
Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu
Dana, I have done some recon-all in NPH patients and didn't have any problems with NPH with large ventricles.
Best Regards
PPJ
----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br
2009/4/16 Dana W. Moore dwm2003@med.cornell.edu
I am trying to use FreeSurfer to measure ventricular volume among patients with normal pressure hydrocephalus. I have run the first subject, whose ventricles are huge. When looking at the subcortical segmentation (aseg.mgz) in tkmedit, I saw that large portions of the ventricles are labeled as cerebral white matter or white matter hypointensities. I tried filling in the ventricles in the wm.mgz volume and then running autorecon2-wm, but this does not appear to have changed anything in the aseg.mgz segmentation nor in the aseg.stats file. Is there a way I can correct this problem, and/or prevent it when I run more NPH patients?
Thanks, Dana
Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dana,
the really huge ventricle subjects do sometimes fail with the current version. We have some tools in development that work quite nicely for many different ventricle sizes (including huge), but they aren't close to being ready to be distributed. You should be able to edit the aseg.mgz in tkmedit to relabel the ventricles and then rerun from there forward in recon-all.
cheers, Bruce
On Thu, 16 Apr 2009, Dana W. Moore wrote:
I am trying to use FreeSurfer to measure ventricular volume among patients with normal pressure hydrocephalus. I have run the first subject, whose ventricles are huge. When looking at the subcortical segmentation (aseg.mgz) in tkmedit, I saw that large portions of the ventricles are labeled as cerebral white matter or white matter hypointensities. I tried filling in the ventricles in the wm.mgz volume and then running autorecon2-wm, but this does not appear to have changed anything in the aseg.mgz segmentation nor in the aseg.stats file. Is there a way I can correct this problem, and/or prevent it when I run more NPH patients?
Thanks, Dana
Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dana,
There is also a '-bigventricles' flag which you can pass to recon-all, which affects mri_ca_register and mri_ca_label. Not sure of its efficacy though.
Nick
On Thu, 2009-04-16 at 14:54 -0400, Bruce Fischl wrote:
Hi Dana,
the really huge ventricle subjects do sometimes fail with the current version. We have some tools in development that work quite nicely for many different ventricle sizes (including huge), but they aren't close to being ready to be distributed. You should be able to edit the aseg.mgz in tkmedit to relabel the ventricles and then rerun from there forward in recon-all.
cheers, Bruce
On Thu, 16 Apr 2009, Dana W. Moore wrote:
I am trying to use FreeSurfer to measure ventricular volume among patients with normal pressure hydrocephalus. I have run the first subject, whose ventricles are huge. When looking at the subcortical segmentation (aseg.mgz) in tkmedit, I saw that large portions of the ventricles are labeled as cerebral white matter or white matter hypointensities. I tried filling in the ventricles in the wm.mgz volume and then running autorecon2-wm, but this does not appear to have changed anything in the aseg.mgz segmentation nor in the aseg.stats file. Is there a way I can correct this problem, and/or prevent it when I run more NPH patients?
Thanks, Dana
Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Dana W. Moore -
Nick Schmansky -
Pedro Paulo de Magalhães Oliveira Junior