If FSL is not installed, then bbregister should have failed and recon-all should have stopped. Did that not happen?

To answer your question, it might not make any difference. If the flair and T1 were acquired at the same time, then it probably just used the scanner coordinates to do the initial alignment, which was probably pretty good. You can view the registration to see how good it is (and look at the first value in the mincost file, if that is less than .7, is is probably fine)

In the end, if your surfaces look ok, then it fine.

doug

On 5/27/13 8:19 AM, Bruce Fischl wrote:

Hi Veronica

thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug
Bruce
On Mon, 27 May 2013, Popescu, Veronica wrote:

Dear Bruce,
They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each.
My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed?
Best wishes,
Veronica

-----Original Message-----
From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu]
Sent: vrijdag 24 mei 2013 15:59
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed

Hi Veronica

BBR can use FSL or SPM to initialize, although we'll probably add an option
in the future to use some things that Martin Reuter and Christian Wachinger
are working on. How did the refinement work? We've only run it on a handful
of cases, so it's pretty bleeding edge and I'm interested in feedback.

cheers
Bruce

On Fri, 24 May 2013, Popescu, Veronica
wrote:

Dear all,
I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an
error message in the log file (attached) about the FSL installation missing.
How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is
preferable?
Thank you very much in advance!
Best wishes,
Veronica

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