Hello All,
I have run my data through free surfer 5.1. If I run recon-all distributed with free surfer 6 as follows
/Applications/freesurfer6/bin/recon-all -s bert -brainstem-structures
where bert was created using freesurfer 5.1, will it work ?
Best
Ri
----- Original Message ----- From: Eugenio Iglesias e.iglesias@bcbl.eu To: Alan Francis alandarkenergy@gmail.com Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Fri, 11 Dec 2015 12:51:24 -0500 (EST) Subject: Re: [Freesurfer] HSF in 5.3
Hi Alan, the subfield module is not present in 5.3; you'll need to download the development version (or wait until 6.0 is released, which should be pretty soon=. Cheers, Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Alan Francis" alandarkenergy@gmail.com To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu, "eiglesias" eiglesias@bcbl.eu Sent: Friday, December 11, 2015 6:36:42 PM Subject: HSF in 5.3
Hi Eugenio: I am trying to run the HSF method on 42 subjects. The FS version on our cluster is 5.3. However when I use the following command I get an error message.
[alanf@micc alanf]$ recon-all -s Smoke_d004 -hippocampal-subfields
ERROR: Flag -hippocampal-subfields unrecognized.
-s Smoke_d004 -hippocampal-subfields
Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s Smoke_d004 exited with ERRORS at Thu Dec 10 16:54:44 EST 2015
For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I tried adding the -hippocampal-subfields-T1 but that did not work too.
thanks,
Alan