Hi Bruce, Thanks for the quick response. Are there plans to add functionality to label sulcal CSF from T2 images? (Or can I do this easily using some existing script ?) My intuition is that this would be helpful since as brain tissue atrophy occurs in a given neurological disorder (Multiple Sclerosis, aging), one would expect both the ventricular and the sulcal CSF volumes to increase and that we would get a lower estimate of atrophy by measuring only the ventricular CSF ?
Regards, Mehul On 7/19/07, Bruce Fischl <[EMAIL PROTECTED]> wrote:
Hi Mehul, We explicitly label ventricular CSF, but not sulcal CSF (which you pretty much can't do from only a T1 volume). The ICV would give you an approximation of the sum of it all, so yes I think what you are doing is a reasonable approach. cheers, Bruce On Thu, 19 Jul 2007, Mehul Sampat wrote: > Hi > > I am interested in measuring the Brain Parenchymal Fraction (BPF) which is > defined as follows: > > BPF = (total White Matter (WM) Volume + total Gray Matter (GM) Volume) / > (total White Matter Volume (WM) + total Gray Matter Volume (GM)+ total CSF > volume) > > I think I get the White and Gray Matter Volumes for each hemisphere from the > command: mris_anatomical_stats. > I think the denominator in the BPF equation is just the Intracranial > Volume, reported in the aseg.stats file > > Would this be an appropriate way to measure these volumes ? > Thanks > Mehul > p.s: For the subject bert the BPF = 1661478/1799364 = 0.92 > > > On 6/25/07, Bruce Fischl <[EMAIL PROTECTED] > wrote: >> >> Hi Antonio, >> >> that's why we we use the surfaces for white matter and cortical gray >> matter volume. >> >> cheers, >> Bruce >> On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: >> >> > Hi Bruce, >> > Thank you for your quick response. >> > >> > Our problem, actually, is that when we visualize the aseg.mgz volume >> > (with color-coded subcortical structures) we see that WM is classified >> > as GM (left circle around insula in the figure) and GM is classified as >> > WM (right lower circle in the figure). >> > So, even if the surfaces look good, we are worried about the effects of >> > this misclassification on volume measurements in aseg.mgz. >> > >> > Thanks, >> > >> > Antonio >> > >> > >> > >> >> -----Original Message----- >> >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] ] >> >> Sent: Monday, June 25, 2007 4:10 PM >> >> To: Gallo, Antonio (NIH/NINDS) [F] >> >> Cc: freesurfer@nmr.mgh.harvard.edu >> >> Subject: Re: [Freesurfer] Segmentation >> >> >> >> Hi Antonio, >> >> >> >> I wouldn't use the wm.mgz for much of anything. It's really just an >> >> intermediate step in the creation of the surfaces. In general we trust >> > the >> >> ?h.white and ?h.pial surfaces first, then the aseg.mgz for things like >> >> hippocampus, ventricles, etc... >> >> >> >> Bruce >> >> >> >> >> >> On Mon, 25 Jun 2007, Gallo, Antonio (NIH/NINDS) [F] wrote: >> >> >> >>> Hi All, >> >>> >> >>> Upon reviewing subortical segmentations I see that often a mismatch >> >>> exists between what appears on the wm.mgz and the color-coded >> > segmented >> >>> maps. >> >>> >> >>> Precisely - as an example - in the attached figure you can see that >> > in >> >>> the case of left insula WM, part of the tissue was classified as GM >> > (in >> >>> brown) in the color-coded segmented map and as WM in the wm.mgz. >> >>> Contrariwise, the right temporal-parietal GM cortex part of the >> > tissue >> >>> is classified as WM (in green) the color-coded segmented map and as >> >>> non-WM in the wm.mgz. The latter occurs in many regions of the brain >> >>> without a clear anatomical pattern. >> >>> >> >>> >> >>> >> >>> I was wondering if this is just a display issue or it rather reflects >> >>> some mismatch in actual tissue classification with consequential >> > errors >> >>> in the generated values of thickness and volumes as well? >> >>> >> >>> If so, is there any way I can correct for this? >> >>> >> >>> >> >>> >> >>> Thank you in advance, >> >>> >> >>> >> >>> >> >>> Antonio >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> Antonio Gallo, MD >> >>> >> >>> NIB-NINDS-NIH >> >>> >> >>> 10 Center Drive >> >>> >> >>> Building 10, Room 5B16 >> >>> >> >>> Bethesda, MD, 20892 - USA >> >>> >> >>> ph #: 001-301-402.6391 >> >>> >> >>> fax #: 001-301-402.0373 >> >>> >> >>> *********************** >> >>> >> >>> >> >>> >> >>> >> > >> > _______________________________________________ >> > 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
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