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
