in v5.1, the talairach stage was moved to precede the nu_correct stage, so that creation of nu.mgz can benefit from usage of the talairach.xfm. this means that the talairach stage uses orig.mgz as input instead of nu.mgz (the nu_correct'd image). in looking at your talairach images, they seem good enough for freesurfer purposes, but clearly are not as good as v5.0. they seems sufficient for ICV as long as ICV is used as normalizer for, say, hippocampal volume, in a group study. the freesurfer ICV is not a very accurate absolute measure (see wiki on how its calculated).

i suppose we could run the talairach stage again after nu.mgz is created, since the talairach stage only takes a couple minutes.

n.

On Mon, 2011-09-19 at 10:25 -0500, Koller, Jonathan wrote:

Hi Ed and freesurfer folks,

Thanks for your reply, but I think that the ICV is computed from talairach.xfm (see lines 3261-3266 in the current recon-all), which is actually computed before any normalization. If you look at file times, talairach.xfm (in the mri/transforms/ directory) is created right after orig.mgz, and before nu.mgz. The input for the 12-parameter talairach registration is the orig.mgz image (converted to analyze, and then 4dfp format). Is this not the case?

Thanks,

Jon

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Ed Gronenschild Sent: Saturday, September 17, 2011 2:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ICV differences from version 5.0 to 5.1

Jon,

The reason is that already in one step earlier in the pipeline,

the nu-correct stage, a difference arises. See thread on

"Differences in nu.mgz between v5.0.0 and v5.1.0"

Cheers,

Ed

    Hi,



    We have noticed differences in Talairach registration (and
    therefore ICV estimates) in some of our subjects from version
    5.0 to version 5.1. Please see the attached document. There
    are 4 subjects, each row represents the same subject, same
    input images, same recon-all options (-all) between versions.
    The bottom of the second page has a table with the ICV values
    for these subjects across versions.



    Have there been any changes to the Talairach registration step
    from 5.0 to 5.1 that would account for these differences?



    Thanks,

    Jon

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