Great. Also, thanks so much for the Wiki entry on persistent edits. Looks like I could create an experts options file from the info contained in my recon-all.log to preserve any command line flags used in earlier versions of FS. Is the -notal-check flag required if used in an earlier FS version? From the wiki, it looks like an existing talairach.xfm file might keep the stream running (rather than stopping) at the tal check stage...but of course this depends on whether the tal check looks for that file before running the check...

Any clarification is greatly appreciated Jenifer

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, September 22, 2010 6:51 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -legacy

yes, the -legacy flag was only necessary for the v3.0 to v4.0 transition. v4.0 data should be fully compatible with reprocessing in v5.

n.

On Wed, 2010-09-22 at 17:31 -0500, Juranek, Jenifer wrote:

I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't look like a legacy analysis (see below). [jjuranek@localhost subjects]$ recon-all -legacy -s SB_057_H21001 ERROR: you have specified -legacy, but this does not look like a legacy analysis.

My recon-all.log file for this subjid reports the following build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5

How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? Have I skipped too many versions to use this -legacy flag?

Many thanks, Jenifer

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