If the FLAIR was acquired in the same session you might be ok, as bbregister inititialized from the headers will be close enough unless there is large-scale movement between scans. Bruce
On Tue, 28 May 2013, Popescu, Veronica wrote:
Dear all, How "fatal" is the FSL environment not being initialized for FreeSurfer 5.3 with FLAIR refinement? I do get results (which look good). Should I rerun them with FSL installed? Thank you very much in advance! Sincerely, Veronica
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: maandag 27 mei 2013 14:19 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] recon-all with FLAIR error no FSL installed
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer