It certainly is my read of the Buckner 2004 paper that they used skull- stripped brains in their registration.
>From the last paragraph of page 724: "Registration was driven by the brain as a loose-fitting mask was applied to exclude skull and extracranial features." What was the original motivation for deriving your own estimate of the scaling factor to convert the determinant to a volume estimate? -Mike H. On Thu, 2008-09-04 at 09:24 -0400, Bruce Fischl wrote: > Hi Mike, > > the alignment whole head is used to determine the atlas scaling factor, > which itself was computed using some manually generated ICV values. Did > Randy use skull-stripped brains? I didn't remember that and would have > thought that defeated the purpose since you'll strip the sulcal CSF as well > from only a T1 image. I'll have to go look at that paper again (or ask > Randy :>) > > Bruce > > On Thu, 4 Sep > 2008, Michael Harms wrote: > > > > > Now I've become confused. > > > > ICV is based on the determinant of talaiarach_with_skull.lta, for which > > the skull is not stripped. So, I've always assumed that basically > > everything -- wm, gm, csf, cerebellum, dura, AND skull tissue -- all > > "contribute" to the definition of the transform (using whatever cost > > metric that the lta registration uses). > > > > Is this correct? If so, a question I've had for some time is to what > > extent the skull itself (and not the wm, gm, csf, cerebellum) drives the > > talaiarach_with_skull.lta transform, since in principle, shouldn't an > > intra-cranial volume estimate be determined solely by the skull? > > > > It is also probably worth noting that this approach for ICV estimation > > is motivated by Buckner 2004, which actually computed the transform > > using a skull-stripped volume. I've always assumed that this is part of > > the reason that the FS folks derived their own scaling factor (for > > converting the determinant to an actual volume estimate) in a sample of > > 22 brains, rather than using the scale factor from the Buckner paper, > > which had a much larger sample (147 subjects). Notably, the two > > different scale factor differ considerably (2150 in FS vs. 1738 in the > > Buckner paper). Whether this is due to the use of skull-stripped vs. > > non-skull-stripped volumes in the registrations, or rather reflects an > > artifact of different populations (and a potentially less generalizable > > FS scale factor due to the much smaller N) remains to be established, > > correct? > > > > thanks for clarifying, > > Mike H. > > > > On Thu, 2008-09-04 at 07:48 -0400, Bruce Fischl wrote: > >> yes, that's correct. > >> > >> Bruce > >> On Wed, 3 Sep 2008, Jeff Sadino wrote: > >> > >>> > >>> Hello, > >>> > >>> I am measuring the shrinkage of the limbic system over time for several > >>> subjects and need to know what is included in the ICV value in aseg.stats > >>> to do this. We are putting our raw scans into freesurfer without any > >>> manual edits until after QA at the end. My understanding is that the > >>> brain gets registered to the talairach template, the skull gets stripped, > >>> and then everything inside the skull - wm, gm, csf, cerebellum - gets > >>> included in the ICV (via scaling of the determinant of > >>> talairach_with_skull.lta)? Can someone confirm this work flow for us? > >>> > >>> Thank you very much, > >>> Jeff > >>> _________________________________________________________________ > >>> See how Windows Mobile brings your life together?at home, work, or on the > >>> go. > >>> http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ > >>> _______________________________________________ > >>> 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
