Re: [Freesurfer] ICV differences from version 5.0 to 5.1

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