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
