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
pgreenberg@ucsd.edu
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 

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
pgreenberg@ucsd.edu