Here is an approach that will be easier, and involves less back and forth between the surface and volume-based streams (and thus should be more accurate): Just use 'mris_volume' to get the volume of everything enclosed by the pial surface, which if I recall correctly will include the lateral ventricles, choroid plexus, and usually most of the inferior lateral ventricles (but not the 3rd and 4th ventricles). Then, if you want to exclude ventricles from your definition of "brain volume", just subtract the Lateral-Ventricle, choroid-plexus, and Inf-Lat-Vent volumes (taken from the aseg.stats).
cheers, Mike H.
On Fri, 2010-01-08 at 15:13 -0500, Xiangchuan Chen wrote:
Dear FreeSurfer experts,
After searching on FreeSurfer wiki and mailing list, I know that the ICV reported in aseg.stats is an estimated value based on talairach transformation. So, if the talairach transformation for a subject's head is not good, the ICV for this subject is not accurate, am I right?
If this is the case, it may not be suitable to use ICV to adjust the volumetric data in aseg.stats and ?h.aparc.stats for some special subjects. I am thinking of using "brain volume" for this purpose. Here are the steps to get it:
Get the surface-based volume of cerebral white matter (aseg.stats).
Add up the volumes of all cortical regions to get the surface-based
volume of cerebral cortex (aparc.stats).
- Add up the above volumes (including both hemispheres) and the volumes of
all other regions listed in aseg.stats (except for cerebral white matter and cerebral cortex) to get the brain volume.
Is this a suitable way to obtain more accurate brain volume?
Thanks in advance and any suggestions are greatly appreciated,
Xiangchuan Chen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mike,
Thanks for your suggestions. I have learned this idea from previous posts (including yours), but found that there is an issue for this approach when I checked the pial surface with tkmedit (tkmedit subjid T1.mgz lh.pial -aux-surface rh.pial): part of two important brain structures, amygdala and hippocampus, is not enclosed in the pial surface. Is there a way to resolve this issue?
Thanks, Xiangchuan
-----Original Message----- From: Michael Harms [mailto:mharms@conte.wustl.edu] Sent: Friday, January 08, 2010 15:55 To: Xiangchuan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ICV/brain volume
Here is an approach that will be easier, and involves less back and forth between the surface and volume-based streams (and thus should be more accurate): Just use 'mris_volume' to get the volume of everything enclosed by the pial surface, which if I recall correctly will include the lateral ventricles, choroid plexus, and usually most of the inferior lateral ventricles (but not the 3rd and 4th ventricles). Then, if you want to exclude ventricles from your definition of "brain volume", just subtract the Lateral-Ventricle, choroid-plexus, and Inf-Lat-Vent volumes (taken from the aseg.stats).
cheers, Mike H.
On Fri, 2010-01-08 at 15:13 -0500, Xiangchuan Chen wrote:
Dear FreeSurfer experts,
After searching on FreeSurfer wiki and mailing list, I know that the ICV reported in aseg.stats is an estimated value based on talairach transformation. So, if the talairach transformation for a subject's head
is
not good, the ICV for this subject is not accurate, am I right?
If this is the case, it may not be suitable to use ICV to adjust the volumetric data in aseg.stats and ?h.aparc.stats for some special
subjects.
I am thinking of using "brain volume" for this purpose. Here are the steps to get it:
Get the surface-based volume of cerebral white matter (aseg.stats).
Add up the volumes of all cortical regions to get the surface-based
volume of cerebral cortex (aparc.stats).
- Add up the above volumes (including both hemispheres) and the volumes
of
all other regions listed in aseg.stats (except for cerebral white matter
and
cerebral cortex) to get the brain volume.
Is this a suitable way to obtain more accurate brain volume?
Thanks in advance and any suggestions are greatly appreciated,
Xiangchuan Chen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Michael Harms -
Xiangchuan Chen