I have included a script to export these values to a spreadsheet http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/excelICV-aseg
2008/9/4 Bruce Fischl <[EMAIL PROTECTED]> > p.s. we probably do something similar to the "loose-fitting mask" as we > only use non-brain locations that are reasonably close to brain (within 2 cm > or so) > > On Thu, 4 Sep 2008, Michael Harms wrote: > > >> 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 > -- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom
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