Hi yes, the FS ICVs mostly seem to work :-)
I still think one should watch out for outliers. We had a sample of 28 kids aged 8-13 yrs, and the ICVs were quite a bit off and useless for two of those, so I would check all carefully especially if you have a group that may have smaller than normal adult ICV. Best, K > Hi, for those interested: we have correlated FS's ICV estimates and > estimates from a procedure developed by Anders Dale (a deformable template > procedure, similar to the Shrink Wrapping procedure previously described > by Dale and colleagues (Dale et al, 1999; Dale and Sereno, 1993)). > > Mean ICV from FS: 1567690 (SD = 161247) > Mean ICV from Dale: 1584008 (SD = 136979) > > The difference was not significant (p = .12, t = -1.596) > > The correlation was .84. A scatterplot is attached (FS on the y-axis, > Dale's method on the x). > > Not too bad, but not perfect either. > > The sample was a life-span sample (20-90 years, n = 74). > > Hope this info was usefull. > > Best, > Anders MF > > > > >> >> Hi Paul, >> Just as an aside, once you have a talairach_with_skull.lta file (whether >> from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), >> where the scale_factor employed is 2150. >> >> Incidentally, using the -eTIV option of mri_label_volume, you can also >> specify other transforms (e.g., talairach.xfm, talairach.lta) to be used >> used instead of the default talairach_with_skull.lta in computing "ICV". >> I've looked at the effect of using different transforms in a handful of >> brains, and "ICV" can vary a bit depending on transform you choose to >> use. >> >> I'm curious: Has anyone out there compared FS's ICV estimate to ICV >> estimated by another program? >> >> Best, >> Mike H. >> >> >> On Fri, 2008-06-20 at 14:35 -0700, Paul Greenberg wrote: >>> Hello Freesurfers, >>> >>> I am interested in comparing eTIV calculated with version 3.0.5 to >>> that calculated by version 4.0.5 (64 bit Cent OS). >>> >>> In order to compare eTIV for a single brain estimated in version 3.0.5 >>> to version 4.0.5, I copied a subject's previous freesurfer output >>> (v3.0.5) into the freesurfer version 4.0.5 folder, deleted all the >>> files within the "transforms" folder and carried out the following >>> procedures as outlined in the recon-all dev table: >>> >>> 1) Run the talairach procedure. Command = talairach_avi --i >>> mysubject --xfm talairach.auto.xfm >>> 2) cp talairach.auto.xfm talairach.xfm >>> 3) Run automatic failure detection. Command= talairach_afd -T 0.005 >>> -xfm talairach.xfm >>> 4) Create talairach_with_skull.lta. Command = >>> mri_em_register -skull nu.mgz >>> $freesurferhome/average/RB_all_withskull_2007-08-08.gca >>> talairach_with_skull.lta >>> 5) Check the new eTIV. Command = >>> mri_label_volume -eTIV talairach_with_skull.lta aseg.mgz 17 53 >>> As the aseg.mgz file exists from previous processing (versio >>> 3.0.5), and the talairach_with_skull.lta was re-created with the new >>> processing (version 4.0.5), the output of this command should list the >>> eTIV based on the new talairach transform? >>> >>> Are these procedures correct for generating new values of eTIV if that >>> is all i want? >>> >>> Thanks! >>> >>> -- >>> >>> Paul Greenberg, Ph.D. >>> Radiology Department, University of California, San Diego >>> VA San Diego Healthcare System (116A-13) >>> 3350 La Jolla Village Drive >>> San Diego, CA 92161 >>> Phone: (858) 552-8585 ext. 2903 >>> Fax: (858) 642-3836 >>> [EMAIL PROTECTED] >>> _______________________________________________ >>> 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
