or you could use mris_wm_volume, which excludes the interior of the ventricles and gray matter structures, and mris_volume and the aseg to calculate it (adding the structures you are interested back in). Maybe we should start generating this # by default. Would enough people find it useful?
cheers, Bruce On Sat, 9 Jan 2010, Michael Harms wrote: > > You're correct that a small amount of hippocampus and amygdala falls > outside the pial surface. However, it will be a TINY percentage of the > whole brain volume, and MUCH smaller than variation of brain volume across > individuals. So the little bit of hippocampus and amygdala that is > "missed" will be inconsequential in my opinion. > > cheers, > Mike H. > >> 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:mha...@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: >>> >>> 1. Get the surface-based volume of cerebral white matter (aseg.stats). >>> >>> 2. Add up the volumes of all cortical regions to get the surface-based >>> volume of cerebral cortex (aparc.stats). >>> >>> 3. 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 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
