Hi Robert, I think Nick misspoke/miswrote. The aseg.stats will be the same between 5.2 and 5.3 even if you did not run the command below to update your 5.2 subjects. After you run that command, your 5.2 subject will be identical to if you re-ran that subject from the beginning with 5.3. If you ran it with -autorecon2 -autorecon3 instead of the command below, you are still safe because -autorecon2 runs -white -smooth2 -inflate2
doug
On 06/05/2013 10:26 AM, Welsh, Robert wrote:
Hi Nick,
Question about your statement below of: ". . .but our tests show this difference to be insignificant."
Would that mean it is safe to assume that if to take some of our brains from FS 5.2 to FS 5.3 we used "-autorecon2 -autorecon3" and then some of our brains were upgraded to FS 5.3 with the flags you list below "-white . . . -autorecon3" we would still be okay with doing comparisons? Unfortunately we started one batch (which is predominately from one of our cohorts) with "-autorrecon2 -autorecon3" before I saw this message below.
Hopefully, we have not introduced a cohort by recon-all flag bias.
Thanks,
-Robert
On 5/15/13 4:14 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Freesurfers,
The new version of Freesurfer, v5.3, is available for download!
Recall from our prior posting that this is intended to replace v5.2, which had a problem with pial and white surface generation affecting thickness and area measures. Users should not use v5.2 for any surface-based studies.
For a list of what v5.3 contains, see this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
If you have already run data through v5.2, and do not want to re-run everything again but only what is necessary, then run the following on your subjects using v5.3:
recon-all -s <subjid> \ -white \ -smooth2 \ -inflate2 \ -autorecon3
This will create new surfaces and surface data. Note that if you choose to re-run the entire stream (-all), the aseg stats will differ from v5.2, but our tests show this difference to be insignificant.
To download v5.3, see this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
And remember our home page is here:
http://surfer.nmr.mgh.harvard.edu
And list info is here:
http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you to everyone who downloaded and tested the beta release of v5.3. We apologize for the hassle and expense of releasing a problematic v5.2. We have improved our testing in the process.
The Freesurfites
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