Dear FreeSurfers,
I wanted just eTIV from a bunch of subjects, and it looked to me from an example log file that both old (with skull) and new (without) estimates would be available after autorecon1, since registration with and without skull seems to have been performed early on. However, I've noticed that the results of both old and new differ from one run of just -autorecon1 versus one of -all:
$ mri_segstats --old-etiv-only --subject ALL atlas_icv (eTIV) = 1465825 mm^3 (det: 1.466751 ) $ mri_segstats --old-etiv-only --subject RECON1 atlas_icv (eTIV) = 1453815 mm^3 (det: 1.478867 )
$ mri_segstats --etiv-only --subject ALL atlas_icv (eTIV) = 1368231 mm^3 (det: 1.423813 ) $ mri_segstats --etiv-only --subject RECON1 atlas_icv (eTIV) = 1360078 mm^3 (det: 1.432349 )
The above are using FS v.4.5. I've also noticed that none of the above exactly reproduce some results that someone else in my lab previously found with FS v.4.03, though I'm not sure whether they changed some of the expert parameters/options or not...
$ mri_segstats --old-etiv-only --subject v403 atlas_icv (eTIV) = 1449214 mm^3 (det: 1.483562 ) $ mri_segstats --etiv-only --subject v403 atlas_icv (eTIV) = 1366893 mm^3 (det: 1.425207 )
If parameters were the same, should I expect old-etiv-only to be consistent before and after v4.3 when the default changed, or did some other things relevant to eTIV change too?
Finally, if I just want TIV estimates, but these might be more accurate after -all than -autorecon1, is there a simple combination of -autorecon1 with some extra directives that would reproduce those from -all without doing all of the really time-consuming cortical stuff?
Many thanks, Ged