If you want to establish that the changes in a given region are in excess of any global atropy, then yes, I would agree that you want to use a measure of brain volume rather than ICV as a covariate.
-MH > Hi Martin, Bruce and Mike, > > Thank you for all your suggestions. > > For Martin's suggestion: I found that it is hard to really fix the > talairach > transform for a lot of my subjects. In most cases, I tried to match the > outlines between target and moveable images when running "tkregister2 > --mgz > --fstal --s subjid" (step1). For some of these subjects, I also checked > the > talairach transform by running "tkregister2 --xfm talairach.xfm --targ > $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov > ../nu_noneck.mgz --reg junk" (step2), and found that the moveable and > target > images were not aligned very well (looked worse than in step1). In this > case, do I need to further edit the talairach transform in step2? > > The reason for adjusting with total brain volume: In our study, we found > difference in ICV and a lot of cortical and sub-cortical regions between > groups. Then, we want to know if some of these regions showed extra effect > than other regions. For this purpose, using total brain volume (sum of > effects on these regions) may be better than using ICV (sum of effects, > but > is estimated). Please correct me if I am wrong here. > > For Bruce's suggestion: the cerebral white matter volume (calculated with > mris_wm_volume) is already in aseg.stats. Is there a way to calculate the > cerebral gray matter volume (surface based, more accurate)? I assume that > I > can use the sum of the volumes from aparc.stats. > > Thanks, > Xiangchuan > > >> -----Original Message----- >> From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu] >> Sent: Saturday, January 09, 2010 13:34 >> To: Bruce Fischl >> Cc: Michael Harms; Xiangchuan Chen; freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] ICV/brain volume >> >> Or you can fix the talairach transform and get the icv the standart way. >> >> When dividing by total brain vol, you undo atrophy. That's why icv is >> used. >> >> Martin >> >> On Jan 9, 2010, at 13:01, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> >> > 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 >> > >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
