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 >
ICV_scatters.pdf
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