Hi, I was just seeking some clarification re: the legacy flag in recon-all. Can I use it on subjects procssed with older versions of Freesurfer to reconstruct surfaces that will be consistent with those generated with older versions (i.e., I can collapse data from the two versions), or is the legacy flag intended to allow new versions of recon-all to be used on old data, effectively 'updating' the surfaces (meaning they should not be analyzed together with data generated using older versions). Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Hi Alex,
The legacy flag needs to be used with old data (pre version 3) in order to "update" it to version three compatible data. You want to specifically keep pre version 3 data separate from version 3 data, as folding patterns and atlases are intrinsically different.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Fornito, Alexander Sent: Sunday, February 11, 2007 10:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Legacy flag
Hi, I was just seeking some clarification re: the legacy flag in recon-all. Can I use it on subjects procssed with older versions of Freesurfer to reconstruct surfaces that will be consistent with those generated with older versions (i.e., I can collapse data from the two versions), or is the legacy flag intended to allow new versions of recon-all to be used on old data, effectively 'updating' the surfaces (meaning they should not be analyzed together with data generated using older versions). Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
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Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Alex,
You should be ok with combining data from these three versions.
Although you may want to consult the Release Notes: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes to make sure that the bug fixes in 3.0.4 and 3.0.5 do not affect your work.
Nick
On Fri, 2007-03-16 at 13:56 +1100, Fornito, Alexander wrote:
Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Alex,
you should reprocess everything with the same version. It should be all automatic (all edits should be preserved). Bruce
On Fri, 16 Mar 2007, Fornito, Alexander wrote:
Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick, I've noticed the release notes for v. 3.04 state "Fixed bug whereby the pial surface can cross the midline in the cingulate/callosum area to the other hemisphere. This change will affect the thickness calculations for this area". If I have some data already processed with v. 3.03, could I simply run autorecon2-pial with 3.04 (or 3.05) to make the surfaces comparable?
Thanks again, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
________________________________
From: Fornito, Alexander Sent: Fri 3/16/2007 1:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Version compatability
Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
Alex,
In principle, yes, you could process the data again using the autorecon2-pial flag. But in practice, as Bruce has mentioned in a prior email, it is best to process all subjects in a study with the same version of Freesurfer. Also, there is the issue of the validity of the thickness measurements in this midline region, although Bruce would have to comment on that. Are you interested in the thickness measurements in that region?
Nick
On Mon, 2007-03-19 at 09:01 +1100, Fornito, Alexander wrote:
Hi Nick, I've noticed the release notes for v. 3.04 state "Fixed bug whereby the pial surface can cross the midline in the cingulate/callosum area to the other hemisphere. This change will affect the thickness calculations for this area". If I have some data already processed with v. 3.03, could I simply run autorecon2-pial with 3.04 (or 3.05) to make the surfaces comparable?
Thanks again, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
From: Fornito, Alexander Sent: Fri 3/16/2007 1:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Version compatability
Hi, Is it a problem combining results from data processed using versions 3.03, 3.04, and 3.05? I have some data processed on 3.03 but I'm updating other machines and I'd like to install 3.05. Thanks, Alex
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito@wh.org.au
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